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[companion gist to bioc-devel email titled:] regionReport error leads to ggbio & biovizBase issues, confusingly not on all OS though. See https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016532.html
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$ R CMD build --keep-empty-dirs --no-resave-data regionReport | |
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help | |
* checking for file ‘regionReport/DESCRIPTION’ ... OK | |
* preparing ‘regionReport’: | |
* checking DESCRIPTION meta-information ... OK | |
* installing the package to build vignettes | |
* creating vignettes ... ERROR | |
--- re-building ‘bumphunterExample.Rmd’ using rmarkdown | |
[WARNING] This document format requires a nonempty <title> element. | |
Please specify either 'title' or 'pagetitle' in the metadata. | |
Falling back to 'bumphunterExampleOutput.utf8' | |
--- finished re-building ‘bumphunterExample.Rmd’ | |
--- re-building ‘regionReport.Rmd’ using rmarkdown | |
Warning in citation("TxDb.Hsapiens.UCSC.hg19.knownGene") : | |
no date field in DESCRIPTION file of package 'TxDb.Hsapiens.UCSC.hg19.knownGene' | |
Writing 34 Bibtex entries ... OK | |
Results written to file 'regionReportRef.bib' | |
Warning in getIdeoGR(data) : | |
geom(ideogram) need valid seqlengths information for accurate mapping, | |
now use reduced information as ideogram... | |
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
Quitting from lines 224-229 (basicExploration.Rmd) | |
Error: processing vignette 'regionReport.Rmd' failed with diagnostics: | |
invalid class "ideogramPlot" object: invalid object for slot "height" in class "ideogramPlot": got class "simpleUnit", should be or extend class "numericORunit" | |
--- failed re-building ‘regionReport.Rmd’ | |
"/usr/local/lib/R/bin/Rscript" -e "library(rmarkdown); render('regionReport.Rmd')" | |
Attaching package: ‘BiocStyle’ | |
The following objects are masked from ‘package:rmarkdown’: | |
html_document, md_document, pdf_document | |
processing file: regionReport.Rmd | |
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inline R code fragments | |
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label: installDer (with options) | |
List of 1 | |
$ eval: logi FALSE | |
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label: citation | |
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List of 3 | |
$ echo : logi FALSE | |
$ message: logi FALSE | |
$ warning: logi FALSE | |
Writing 34 Bibtex entries ... OK | |
Results written to file 'regionReportRef.bib' | |
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inline R code fragments | |
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label: overviewNotRun (with options) | |
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label: runDerfinderFake (with options) | |
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label: loadLib (with options) | |
List of 1 | |
$ message: logi FALSE | |
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : | |
running 'make' failed | |
Execution halted | |
Killed | |
> library('regionReport') | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R Under development (unstable) (2020-04-03 r78147) | |
os Debian GNU/Linux 10 (buster) | |
system x86_64, linux-gnu | |
ui X11 | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz Etc/UTC | |
date 2020-04-09 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0) | |
annotate 1.65.1 2020-01-27 [1] Bioconductor | |
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) | |
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0) | |
bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.1.0) | |
Biobase 2.47.3 2020-03-16 [1] Bioconductor | |
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor | |
BiocGenerics 0.33.3 2020-03-23 [1] Bioconductor | |
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0) | |
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor | |
BiocStyle 2.15.6 2020-02-01 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-02 [1] Bioconductor | |
Biostrings 2.55.7 2020-03-24 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
BSgenome 1.55.4 2020-03-19 [1] Bioconductor | |
bumphunter 1.29.0 2019-10-29 [1] Bioconductor | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0) | |
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0) | |
codetools 0.2-16 2018-12-24 [2] CRAN (R 4.1.0) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0) | |
DEFormats 1.15.0 2019-10-29 [1] Bioconductor | |
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor | |
derfinder 1.21.0 2019-10-29 [1] Bioconductor | |
derfinderHelper 1.21.0 2019-10-29 [1] Bioconductor | |
DESeq2 1.27.29 2020-03-17 [1] Bioconductor | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0) | |
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.1.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0) | |
edgeR 3.29.1 2020-02-26 [1] Bioconductor | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0) | |
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0) | |
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.1.0) | |
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0) | |
genefilter 1.69.0 2019-10-29 [1] Bioconductor | |
geneplotter 1.65.0 2019-10-29 [1] Bioconductor | |
generics 0.0.2 2018-11-29 [1] CRAN (R 4.1.0) | |
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor | |
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor | |
GenomicFiles 1.23.2 2020-03-23 [1] Bioconductor | |
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor | |
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.1.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0) | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0) | |
IRanges 2.21.8 2020-03-25 [1] Bioconductor | |
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.1.0) | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0) | |
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.1.0) | |
knitcitations 1.0.10 2019-09-15 [1] CRAN (R 4.1.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0) | |
knitrBootstrap 1.0.2 2018-05-24 [1] CRAN (R 4.1.0) | |
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0) | |
limma 3.43.5 2020-03-06 [1] Bioconductor | |
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.0) | |
lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.1.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0) | |
markdown 1.1 2019-08-07 [1] CRAN (R 4.1.0) | |
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) | |
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0) | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0) | |
qvalue 2.19.0 2019-10-29 [1] Bioconductor | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0) | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0) | |
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0) | |
RefManageR 1.2.12 2019-04-03 [1] CRAN (R 4.1.0) | |
regionReport * 1.21.0 2019-10-29 [1] Bioconductor | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0) | |
rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
rngtools 1.5 2020-01-23 [1] CRAN (R 4.1.0) | |
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0) | |
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0) | |
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor | |
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) | |
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0) | |
xml2 1.3.0 2020-04-01 [1] CRAN (R 4.1.0) | |
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0) | |
XVector 0.27.2 2020-03-24 [1] Bioconductor | |
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0) | |
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor | |
[1] /usr/local/lib/R/site-library | |
[2] /usr/local/lib/R/library |
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## Works well again, thanks to Michael Lawrence for | |
## bumping the version in ggbio with | |
## https://github.com/tengfei/ggbio/commit/6bc94f45e6479b01287e25140821f239f1a7f92d | |
## which includes two commits that fixed things | |
## although only one of them was important for | |
## this issue: | |
## https://github.com/tengfei/ggbio/commit/930e521bfe0967f5095583c69f655fa571e3fa42 | |
## | |
$ R CMD build --keep-empty-dirs --no-resave-data regionReport | |
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help | |
* checking for file ‘regionReport/DESCRIPTION’ ... OK | |
* preparing ‘regionReport’: | |
* checking DESCRIPTION meta-information ... OK | |
* installing the package to build vignettes | |
* creating vignettes ... OK | |
* checking for LF line-endings in source and make files and shell scripts | |
* checking for empty or unneeded directories | |
* building ‘regionReport_1.21.1.tar.gz’ | |
$ R | |
R Under development (unstable) (2020-04-03 r78147) -- "Unsuffered Consequences" | |
Copyright (C) 2020 The R Foundation for Statistical Computing | |
Platform: x86_64-pc-linux-gnu (64-bit) | |
R is free software and comes with ABSOLUTELY NO WARRANTY. | |
You are welcome to redistribute it under certain conditions. | |
Type 'license()' or 'licence()' for distribution details. | |
R is a collaborative project with many contributors. | |
Type 'contributors()' for more information and | |
'citation()' on how to cite R or R packages in publications. | |
Type 'demo()' for some demos, 'help()' for on-line help, or | |
'help.start()' for an HTML browser interface to help. | |
Type 'q()' to quit R. | |
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help | |
> library('regionReport') | |
> library('ggbio') | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: ‘BiocGenerics’ | |
The following objects are masked from ‘package:parallel’: | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, | |
parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB | |
The following objects are masked from ‘package:stats’: | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from ‘package:base’: | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, | |
evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, | |
paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, | |
table, tapply, union, unique, unsplit, which, which.max, which.min | |
Loading required package: ggplot2 | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
Need specific help about ggbio? try mailing | |
the maintainer or visit http://tengfei.github.com/ggbio/ | |
Attaching package: 'ggbio' | |
The following objects are masked from 'package:ggplot2': | |
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim | |
> library('sessioninfo') | |
> options(width = 120) | |
> session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R Under development (unstable) (2020-04-03 r78147) | |
os Debian GNU/Linux 10 (buster) | |
system x86_64, linux-gnu | |
ui X11 | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz Etc/UTC | |
date 2020-04-10 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0) | |
annotate 1.65.1 2020-01-27 [1] Bioconductor | |
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor | |
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) | |
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0) | |
bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.1.0) | |
Biobase 2.47.3 2020-03-16 [1] Bioconductor | |
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor | |
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor | |
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0) | |
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor | |
BiocStyle 2.15.6 2020-02-01 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-02 [1] Bioconductor | |
Biostrings 2.55.7 2020-03-24 [1] Bioconductor | |
biovizBase 1.35.1 2019-12-03 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
BSgenome 1.55.4 2020-03-19 [1] Bioconductor | |
bumphunter 1.29.0 2019-10-29 [1] Bioconductor | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0) | |
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0) | |
codetools 0.2-16 2018-12-24 [2] CRAN (R 4.1.0) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0) | |
DEFormats 1.15.0 2019-10-29 [1] Bioconductor | |
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor | |
derfinder 1.21.0 2019-10-29 [1] Bioconductor | |
derfinderHelper 1.21.0 2019-10-29 [1] Bioconductor | |
DESeq2 1.27.29 2020-03-17 [1] Bioconductor | |
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0) | |
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.1.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0) | |
edgeR 3.29.1 2020-02-26 [1] Bioconductor | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0) | |
ensembldb 2.11.3 2020-01-22 [1] Bioconductor | |
evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0) | |
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.1.0) | |
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0) | |
genefilter 1.69.0 2019-10-29 [1] Bioconductor | |
geneplotter 1.65.0 2019-10-29 [1] Bioconductor | |
generics 0.0.2 2018-11-29 [1] CRAN (R 4.1.0) | |
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor | |
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor | |
GenomicFiles 1.23.2 2020-03-23 [1] Bioconductor | |
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor | |
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0) | |
ggbio * 1.35.2 2020-04-10 [1] Github (tengfei/ggbio@6bc94f4) | |
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.1.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0) | |
graph 1.65.2 2020-03-17 [1] Bioconductor | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0) | |
IRanges 2.21.8 2020-03-25 [1] Bioconductor | |
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.1.0) | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0) | |
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.1.0) | |
knitcitations 1.0.10 2019-09-15 [1] CRAN (R 4.1.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0) | |
knitrBootstrap 1.0.2 2018-05-24 [1] CRAN (R 4.1.0) | |
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0) | |
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0) | |
limma 3.43.5 2020-03-06 [1] Bioconductor | |
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.0) | |
lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.1.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0) | |
markdown 1.1 2019-08-07 [1] CRAN (R 4.1.0) | |
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) | |
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0) | |
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) | |
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0) | |
qvalue 2.19.0 2019-10-29 [1] Bioconductor | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0) | |
RBGL 1.63.1 2019-10-30 [1] Bioconductor | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0) | |
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0) | |
RefManageR 1.2.12 2019-04-03 [1] CRAN (R 4.1.0) | |
regionReport * 1.21.0 2019-10-29 [1] Bioconductor | |
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0) | |
rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
rngtools 1.5 2020-01-23 [1] CRAN (R 4.1.0) | |
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0) | |
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0) | |
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor | |
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0) | |
sessioninfo * 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) | |
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0) | |
xml2 1.3.0 2020-04-01 [1] CRAN (R 4.1.0) | |
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0) | |
XVector 0.27.2 2020-03-24 [1] Bioconductor | |
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0) | |
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor | |
[1] /usr/local/lib/R/site-library | |
[2] /usr/local/lib/R/library |
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> library('derfinderPlot') | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
> example('plotCluster') | |
pltCls> ## Load data | |
pltCls> library('derfinder') | |
pltCls> ## Annotate the results with bumphunter::matchGenes() | |
pltCls> library('bumphunter') | |
Loading required package: S4Vectors | |
Loading required package: stats4 | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: 'BiocGenerics' | |
The following objects are masked from 'package:parallel': | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, | |
parSapply, parSapplyLB | |
The following objects are masked from 'package:stats': | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from 'package:base': | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, | |
intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, | |
sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min | |
Attaching package: 'S4Vectors' | |
The following object is masked from 'package:base': | |
expand.grid | |
Loading required package: IRanges | |
Loading required package: GenomeInfoDb | |
Loading required package: GenomicRanges | |
Loading required package: foreach | |
Loading required package: iterators | |
Loading required package: locfit | |
locfit 1.5-9.4 2020-03-24 | |
pltCls> library('TxDb.Hsapiens.UCSC.hg19.knownGene') | |
Loading required package: GenomicFeatures | |
Loading required package: AnnotationDbi | |
Loading required package: Biobase | |
Welcome to Bioconductor | |
Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages | |
'citation("pkgname")'. | |
pltCls> library('org.Hs.eg.db') | |
pltCls> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, | |
pltCls+ annotationPackage = 'org.Hs.eg.db') | |
Getting TSS and TSE. | |
Getting CSS and CSE. | |
Getting exons. | |
Annotating genes. | |
pltCls> annotation <- matchGenes(x = genomeRegions$regions, subject = genes) | |
pltCls> ## Make the plot | |
pltCls> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation, | |
pltCls+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop, | |
pltCls+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene) | |
Parsing transcripts... | |
Parsing exons... | |
Parsing cds... | |
Parsing utrs... | |
------exons... | |
------cdss... | |
------introns... | |
------utr... | |
aggregating... | |
Done | |
Constructing graphics... | |
Error in validObject(.Object) : | |
invalid class "ideogramPlot" object: invalid object for slot "height" in class "ideogramPlot": got class "simpleUnit", should be or extend class "numericORunit" | |
In addition: Warning messages: | |
1: In getIdeoGR(data) : | |
geom(ideogram) need valid seqlengths information for accurate mapping, | |
now use reduced information as ideogram... | |
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
4: `quo_expr()` is deprecated as of rlang 0.2.0. | |
Please use `quo_squash()` instead. | |
This warning is displayed once per session. | |
Error during wrapup: no slot of name "elementType" for this object of class "GRanges" | |
Error: no more error handlers available (recursive errors?); invoking 'abort' restart | |
> | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R Under development (unstable) (2020-04-03 r78147) | |
os Debian GNU/Linux 10 (buster) | |
system x86_64, linux-gnu | |
ui RStudio | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz Etc/UTC | |
date 2020-04-09 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0) | |
AnnotationDbi * 1.49.1 2020-01-25 [1] Bioconductor | |
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) | |
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0) | |
Biobase * 2.47.3 2020-03-16 [1] Bioconductor | |
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor | |
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor | |
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0) | |
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-02 [1] Bioconductor | |
Biostrings 2.55.7 2020-03-24 [1] Bioconductor | |
biovizBase 1.35.1 2019-12-03 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
BSgenome 1.55.4 2020-03-19 [1] Bioconductor | |
bumphunter * 1.29.0 2019-10-29 [1] Bioconductor | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0) | |
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0) | |
codetools 0.2-16 2018-12-24 [2] CRAN (R 4.1.0) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0) | |
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor | |
derfinder * 1.21.0 2019-10-29 [1] Bioconductor | |
derfinderHelper 1.21.0 2019-10-29 [1] Bioconductor | |
derfinderPlot * 1.21.0 2019-10-29 [1] Bioconductor | |
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0) | |
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.1.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0) | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0) | |
ensembldb 2.11.3 2020-01-22 [1] Bioconductor | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0) | |
foreach * 1.5.0 2020-03-30 [1] CRAN (R 4.1.0) | |
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0) | |
GenomeInfoDb * 1.23.16 2020-03-27 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor | |
GenomicFeatures * 1.39.7 2020-03-19 [1] Bioconductor | |
GenomicFiles 1.23.2 2020-03-23 [1] Bioconductor | |
GenomicRanges * 1.39.3 2020-03-24 [1] Bioconductor | |
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0) | |
ggbio 1.35.1 2020-01-30 [1] Bioconductor | |
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.1.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0) | |
graph 1.65.2 2020-03-17 [1] Bioconductor | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0) | |
IRanges * 2.21.8 2020-03-25 [1] Bioconductor | |
iterators * 1.0.12 2019-07-26 [1] CRAN (R 4.1.0) | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0) | |
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0) | |
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0) | |
limma 3.43.5 2020-03-06 [1] Bioconductor | |
locfit * 1.5-9.4 2020-03-25 [1] CRAN (R 4.1.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0) | |
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) | |
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0) | |
org.Hs.eg.db * 3.10.0 2020-04-09 [1] Bioconductor | |
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) | |
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0) | |
qvalue 2.19.0 2019-10-29 [1] Bioconductor | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0) | |
RBGL 1.63.1 2019-10-30 [1] Bioconductor | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0) | |
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0) | |
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0) | |
rngtools 1.5 2020-01-23 [1] CRAN (R 4.1.0) | |
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0) | |
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0) | |
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor | |
S4Vectors * 0.25.15 2020-04-04 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) | |
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0) | |
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2020-04-09 [1] Bioconductor | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0) | |
XVector 0.27.2 2020-03-24 [1] Bioconductor | |
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor | |
[1] /usr/local/lib/R/site-library | |
[2] /usr/local/lib/R/library |
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> library('ggbio') | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: ‘BiocGenerics’ | |
The following objects are masked from ‘package:parallel’: | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, | |
parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB | |
The following objects are masked from ‘package:stats’: | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from ‘package:base’: | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, | |
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, | |
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, | |
unique, unsplit, which, which.max, which.min | |
Loading required package: ggplot2 | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
Need specific help about ggbio? try mailing | |
the maintainer or visit http://tengfei.github.com/ggbio/ | |
Attaching package: 'ggbio' | |
The following objects are masked from 'package:ggplot2': | |
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, xlim | |
> data(hg19IdeogramCyto, package = 'biovizBase') | |
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21') | |
Warning messages: | |
1: In getIdeoGR(data) : | |
geom(ideogram) need valid seqlengths information for accurate mapping, | |
now use reduced information as ideogram... | |
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
> tracks(p.ideo) | |
Warning messages: | |
1: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
5: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
6: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
7: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
> | |
> validObject(hg19IdeogramCyto) | |
Error in validObject(hg19IdeogramCyto) : | |
invalid class "GRanges" object: slots in class definition but not in object: "elementType" | |
> | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R Under development (unstable) (2020-04-03 r78147) | |
os Debian GNU/Linux 10 (buster) | |
system x86_64, linux-gnu | |
ui RStudio | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz Etc/UTC | |
date 2020-04-10 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0) | |
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor | |
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) | |
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0) | |
Biobase 2.47.3 2020-03-16 [1] Bioconductor | |
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor | |
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor | |
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0) | |
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-02 [1] Bioconductor | |
Biostrings 2.55.7 2020-03-24 [1] Bioconductor | |
biovizBase 1.35.1 2019-12-03 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
BSgenome 1.55.4 2020-03-19 [1] Bioconductor | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0) | |
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0) | |
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor | |
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0) | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0) | |
ensembldb 2.11.3 2020-01-22 [1] Bioconductor | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0) | |
farver 2.0.3 2020-01-16 [1] CRAN (R 4.1.0) | |
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0) | |
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor | |
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor | |
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor | |
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0) | |
ggbio * 1.35.2 2020-04-10 [1] Github (tengfei/ggbio@6bc94f4) | |
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.1.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0) | |
graph 1.65.2 2020-03-17 [1] Bioconductor | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0) | |
IRanges 2.21.8 2020-03-25 [1] Bioconductor | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0) | |
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0) | |
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0) | |
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) | |
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0) | |
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) | |
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0) | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0) | |
RBGL 1.63.1 2019-10-30 [1] Bioconductor | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0) | |
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0) | |
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0) | |
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0) | |
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0) | |
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor | |
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) | |
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0) | |
XVector 0.27.2 2020-03-24 [1] Bioconductor | |
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor | |
[1] /usr/local/lib/R/site-library | |
[2] /usr/local/lib/R/library | |
> |
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$ R | |
R Under development (unstable) (2020-04-03 r78147) -- "Unsuffered Consequences" | |
Copyright (C) 2020 The R Foundation for Statistical Computing | |
Platform: x86_64-pc-linux-gnu (64-bit) | |
R is free software and comes with ABSOLUTELY NO WARRANTY. | |
You are welcome to redistribute it under certain conditions. | |
Type 'license()' or 'licence()' for distribution details. | |
R is a collaborative project with many contributors. | |
Type 'contributors()' for more information and | |
'citation()' on how to cite R or R packages in publications. | |
Type 'demo()' for some demos, 'help()' for on-line help, or | |
'help.start()' for an HTML browser interface to help. | |
Type 'q()' to quit R. | |
Bioconductor version 3.11 (BiocManager 1.30.10), ?BiocManager::install for help | |
> library('ggbio') | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: ‘BiocGenerics’ | |
The following objects are masked from ‘package:parallel’: | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
clusterExport, clusterMap, parApply, parCapply, parLapply, | |
parLapplyLB, parRapply, parSapply, parSapplyLB | |
The following objects are masked from ‘package:stats’: | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from ‘package:base’: | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, | |
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, | |
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, | |
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, | |
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, | |
union, unique, unsplit, which, which.max, which.min | |
Loading required package: ggplot2 | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
Need specific help about ggbio? try mailing | |
the maintainer or visit http://tengfei.github.com/ggbio/ | |
Attaching package: 'ggbio' | |
The following objects are masked from 'package:ggplot2': | |
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, | |
xlim | |
> data(hg19IdeogramCyto, package = 'biovizBase') | |
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21') | |
Warning messages: | |
1: In getIdeoGR(data) : | |
geom(ideogram) need valid seqlengths information for accurate mapping, | |
now use reduced information as ideogram... | |
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
> tracks(p.ideo) | |
Error in validObject(.Object) : | |
invalid class "ideogramPlot" object: invalid object for slot "height" in class "ideogramPlot": got class "simpleUnit", should be or extend class "numericORunit" | |
> | |
> validObject(hg19IdeogramCyto) | |
Error in validObject(hg19IdeogramCyto) : | |
invalid class "GRanges" object: slots in class definition but not in object: "elementType" | |
> | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R Under development (unstable) (2020-04-03 r78147) | |
os Debian GNU/Linux 10 (buster) | |
system x86_64, linux-gnu | |
ui X11 | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz Etc/UTC | |
date 2020-04-09 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.1.0) | |
AnnotationDbi 1.49.1 2020-01-25 [1] Bioconductor | |
AnnotationFilter 1.11.0 2019-10-29 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.1.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.0) | |
backports 1.1.5 2019-10-02 [1] CRAN (R 4.1.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.1.0) | |
Biobase 2.47.3 2020-03-16 [1] Bioconductor | |
BiocFileCache 1.11.4 2019-12-02 [1] Bioconductor | |
BiocGenerics * 0.33.3 2020-03-23 [1] Bioconductor | |
BiocManager * 1.30.10 2019-11-16 [1] CRAN (R 4.1.0) | |
BiocParallel 1.21.2 2019-12-21 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-02 [1] Bioconductor | |
Biostrings 2.55.7 2020-03-24 [1] Bioconductor | |
biovizBase 1.35.1 2019-12-03 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.1.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.1.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.1.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.1.0) | |
BSgenome 1.55.4 2020-03-19 [1] Bioconductor | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.1.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.1.0) | |
cluster 2.1.0 2019-06-19 [2] CRAN (R 4.1.0) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.1.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.1.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.1.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.1.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.1.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.1.0) | |
DelayedArray 0.13.10 2020-04-06 [1] Bioconductor | |
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.1.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.1.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.1.0) | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.1.0) | |
ensembldb 2.11.3 2020-01-22 [1] Bioconductor | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.1.0) | |
foreign 0.8-77 2020-03-26 [2] CRAN (R 4.1.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.1.0) | |
GenomeInfoDb 1.23.16 2020-03-27 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-09 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-03-24 [1] Bioconductor | |
GenomicFeatures 1.39.7 2020-03-19 [1] Bioconductor | |
GenomicRanges 1.39.3 2020-03-24 [1] Bioconductor | |
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.1.0) | |
ggbio * 1.35.1 2020-01-30 [1] Bioconductor | |
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.1.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.1.0) | |
graph 1.65.2 2020-03-17 [1] Bioconductor | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.1.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.1.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.1.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.1.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.1.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.1.0) | |
IRanges 2.21.8 2020-03-25 [1] Bioconductor | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.1.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.1.0) | |
lattice 0.20-41 2020-04-02 [2] CRAN (R 4.1.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.1.0) | |
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.1.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.1.0) | |
Matrix 1.2-18 2019-11-27 [2] CRAN (R 4.1.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.1.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.1.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0) | |
nnet 7.3-13 2020-02-25 [2] CRAN (R 4.1.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.1.0) | |
OrganismDbi 1.29.1 2020-02-04 [1] Bioconductor | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.1.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0) | |
ProtGenerics 1.19.3 2019-12-25 [1] Bioconductor | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.1.0) | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.1.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.1.0) | |
RBGL 1.63.1 2019-10-30 [1] Bioconductor | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.1.0) | |
Rcpp 1.0.4 2020-03-17 [1] CRAN (R 4.1.0) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.1.0) | |
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.1.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.1.0) | |
rpart 4.1-15 2019-04-12 [2] CRAN (R 4.1.0) | |
Rsamtools 2.3.7 2020-03-18 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.1.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.1.0) | |
rtracklayer 1.47.0 2019-10-29 [1] Bioconductor | |
S4Vectors 0.25.15 2020-04-04 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.1.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.1.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) | |
SummarizedExperiment 1.17.5 2020-03-27 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [2] CRAN (R 4.1.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.1.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.1.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.1.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.1.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.1.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.1.0) | |
XVector 0.27.2 2020-03-24 [1] Bioconductor | |
zlibbioc 1.33.1 2020-01-24 [1] Bioconductor | |
[1] /usr/local/lib/R/site-library | |
[2] /usr/local/lib/R/library |
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### ~/.Rprofile content that applies here: | |
### (relates to the warnings shown and the session info) | |
options( | |
warnPartialMatchArgs = TRUE, | |
warnPartialMatchDollar = TRUE, | |
warnPartialMatchAttr = TRUE | |
) | |
if (interactive()) { | |
suppressMessages(require(devtools)) | |
suppressMessages(require(usethis)) | |
suppressMessages(require(testthat)) | |
suppressMessages(require(colorout)) | |
} | |
$ R CMD build --keep-empty-dirs --no-resave-data regionReport | |
Loading required package: colorout | |
* checking for file ‘regionReport/DESCRIPTION’ ... OK | |
* preparing ‘regionReport’: | |
* checking DESCRIPTION meta-information ... OK | |
* installing the package to build vignettes | |
* creating vignettes ... OK | |
* checking for LF line-endings in source and make files and shell scripts | |
* checking for empty or unneeded directories | |
* building ‘regionReport_1.21.1.tar.gz’ | |
$ R | |
R version 4.0.0 alpha (2020-04-07 r78176) | |
Copyright (C) 2020 The R Foundation for Statistical Computing | |
Platform: x86_64-apple-darwin17.0 (64-bit) | |
R is free software and comes with ABSOLUTELY NO WARRANTY. | |
You are welcome to redistribute it under certain conditions. | |
Type 'license()' or 'licence()' for distribution details. | |
Natural language support but running in an English locale | |
R is a collaborative project with many contributors. | |
Type 'contributors()' for more information and | |
'citation()' on how to cite R or R packages in publications. | |
Type 'demo()' for some demos, 'help()' for on-line help, or | |
'help.start()' for an HTML browser interface to help. | |
Type 'q()' to quit R. | |
Loading required package: colorout | |
> library('regionReport') | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R version 4.0.0 alpha (2020-04-07 r78176) | |
os macOS Catalina 10.15.4 | |
system x86_64, darwin17.0 | |
ui X11 | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz America/New_York | |
date 2020-04-08 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.0.0) | |
annotate 1.65.1 2020-04-07 [1] Bioconductor | |
AnnotationDbi 1.49.1 2020-04-07 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) | |
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0) | |
bibtex 0.4.2.2 2020-01-02 [1] CRAN (R 4.0.0) | |
Biobase 2.47.3 2020-04-07 [1] Bioconductor | |
BiocFileCache 1.11.4 2020-04-07 [1] Bioconductor | |
BiocGenerics 0.33.3 2020-04-07 [1] Bioconductor | |
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0) | |
BiocParallel 1.21.2 2020-04-07 [1] Bioconductor | |
BiocStyle 2.15.6 2020-04-07 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-07 [1] Bioconductor | |
Biostrings 2.55.7 2020-04-07 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0) | |
BSgenome 1.55.4 2020-04-07 [1] Bioconductor | |
bumphunter 1.29.0 2020-04-07 [1] Bioconductor | |
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0) | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0) | |
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0) | |
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0) | |
colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0) | |
DEFormats 1.15.0 2020-04-07 [1] Bioconductor | |
DelayedArray 0.13.10 2020-04-07 [1] Bioconductor | |
derfinder 1.21.0 2020-04-07 [1] Bioconductor | |
derfinderHelper 1.21.0 2020-04-07 [1] Bioconductor | |
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0) | |
DESeq2 1.27.29 2020-04-07 [1] Bioconductor | |
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0) | |
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.0.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0) | |
edgeR 3.29.1 2020-04-07 [1] Bioconductor | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0) | |
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.0) | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0) | |
foreach 1.5.0 2020-03-30 [1] CRAN (R 4.0.0) | |
foreign 0.8-77 2020-03-25 [1] CRAN (R 4.0.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.0.0) | |
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0) | |
genefilter 1.69.0 2020-04-07 [1] Bioconductor | |
geneplotter 1.65.0 2020-04-07 [1] Bioconductor | |
generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.0) | |
GenomeInfoDb 1.23.16 2020-04-07 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-08 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-04-07 [1] Bioconductor | |
GenomicFeatures 1.39.7 2020-04-07 [1] Bioconductor | |
GenomicFiles 1.23.2 2020-04-07 [1] Bioconductor | |
GenomicRanges 1.39.3 2020-04-07 [1] Bioconductor | |
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.0.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0) | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.0.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.0.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0) | |
IRanges 2.21.8 2020-04-07 [1] Bioconductor | |
iterators 1.0.12 2019-07-26 [1] CRAN (R 4.0.0) | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0) | |
jsonlite 1.6.1 2020-02-02 [1] CRAN (R 4.0.0) | |
knitcitations 1.0.10 2019-09-15 [1] CRAN (R 4.0.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0) | |
knitrBootstrap 1.0.2 2018-05-24 [1] CRAN (R 4.0.0) | |
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0) | |
limma 3.43.5 2020-04-07 [1] Bioconductor | |
locfit 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.0) | |
lubridate 1.7.8 2020-04-06 [1] CRAN (R 4.0.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0) | |
markdown 1.1 2019-08-07 [1] CRAN (R 4.0.0) | |
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0) | |
nnet 7.3-13 2020-02-25 [1] CRAN (R 4.0.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0) | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.0.0) | |
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0) | |
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0) | |
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0) | |
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0) | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.0.0) | |
qvalue 2.19.0 2020-04-07 [1] Bioconductor | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0) | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0) | |
Rcpp 1.0.4.6 2020-04-08 [1] Github (RcppCore/Rcpp@a831639) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.0.0) | |
RefManageR 1.2.12 2019-04-03 [1] CRAN (R 4.0.0) | |
regionReport * 1.21.1 2020-04-07 [1] Bioconductor | |
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.0.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0) | |
rmarkdown 2.1 2020-01-20 [1] CRAN (R 4.0.0) | |
rngtools 1.5 2020-01-23 [1] CRAN (R 4.0.0) | |
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.0) | |
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0) | |
Rsamtools 2.3.7 2020-04-07 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0) | |
rtracklayer 1.47.0 2020-04-07 [1] Bioconductor | |
S4Vectors 0.25.15 2020-04-07 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0) | |
SummarizedExperiment 1.17.5 2020-04-07 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [1] CRAN (R 4.0.0) | |
testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.0.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0) | |
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.0.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.0.0) | |
xml2 1.3.0 2020-04-01 [1] CRAN (R 4.0.0) | |
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.0.0) | |
XVector 0.27.2 2020-04-07 [1] Bioconductor | |
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.0) | |
zlibbioc 1.33.1 2020-04-07 [1] Bioconductor | |
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library |
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### ~/.Rprofile content that applies here: | |
### (relates to the warnings shown and the session info) | |
options( | |
warnPartialMatchArgs = TRUE, | |
warnPartialMatchDollar = TRUE, | |
warnPartialMatchAttr = TRUE | |
) | |
if (interactive()) { | |
suppressMessages(require(devtools)) | |
suppressMessages(require(usethis)) | |
suppressMessages(require(testthat)) | |
suppressMessages(require(colorout)) | |
} | |
$ R | |
R version 4.0.0 alpha (2020-04-07 r78176) | |
Copyright (C) 2020 The R Foundation for Statistical Computing | |
Platform: x86_64-apple-darwin17.0 (64-bit) | |
R is free software and comes with ABSOLUTELY NO WARRANTY. | |
You are welcome to redistribute it under certain conditions. | |
Type 'license()' or 'licence()' for distribution details. | |
Natural language support but running in an English locale | |
R is a collaborative project with many contributors. | |
Type 'contributors()' for more information and | |
'citation()' on how to cite R or R packages in publications. | |
Type 'demo()' for some demos, 'help()' for on-line help, or | |
'help.start()' for an HTML browser interface to help. | |
Type 'q()' to quit R. | |
Loading required package: colorout | |
> library('derfinderPlot') | |
apropos('example') | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
> apropos('example') | |
[1] "example" "run_examples" "test_example" | |
[4] "test_examples" "testthat_example" "testthat_examples" | |
> | |
> example( | |
ask= echo= lib.loc= package= run.dontrun= setRNG= verbose= | |
character.only= give.lines= local= prompt.prefix= run.donttest= topic= | |
> example('plotCluster') | |
pltCls> ## Load data | |
pltCls> library('derfinder') | |
pltCls> ## Annotate the results with bumphunter::matchGenes() | |
pltCls> library('bumphunter') | |
Loading required package: S4Vectors | |
Loading required package: stats4 | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: 'BiocGenerics' | |
The following objects are masked from 'package:parallel': | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
clusterExport, clusterMap, parApply, parCapply, parLapply, | |
parLapplyLB, parRapply, parSapply, parSapplyLB | |
The following objects are masked from 'package:stats': | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from 'package:base': | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, | |
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, | |
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, | |
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, | |
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, | |
union, unique, unsplit, which, which.max, which.min | |
Attaching package: 'S4Vectors' | |
The following object is masked from 'package:base': | |
expand.grid | |
Loading required package: IRanges | |
Loading required package: GenomeInfoDb | |
Loading required package: GenomicRanges | |
Loading required package: foreach | |
Loading required package: iterators | |
Loading required package: locfit | |
locfit 1.5-9.4 2020-03-24 | |
pltCls> library('TxDb.Hsapiens.UCSC.hg19.knownGene') | |
Loading required package: GenomicFeatures | |
Loading required package: AnnotationDbi | |
Loading required package: Biobase | |
Welcome to Bioconductor | |
Vignettes contain introductory material; view with | |
'browseVignettes()'. To cite Bioconductor, see | |
'citation("Biobase")', and for packages 'citation("pkgname")'. | |
pltCls> library('org.Hs.eg.db') | |
pltCls> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, | |
pltCls+ annotationPackage = 'org.Hs.eg.db') | |
Getting TSS and TSE. | |
Getting CSS and CSE. | |
Getting exons. | |
Annotating genes. | |
pltCls> annotation <- matchGenes(x = genomeRegions$regions, subject = genes) | |
pltCls> ## Make the plot | |
pltCls> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation, | |
pltCls+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop, | |
pltCls+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene) | |
Parsing transcripts... | |
Parsing exons... | |
Parsing cds... | |
Parsing utrs... | |
------exons... | |
------cdss... | |
------introns... | |
------utr... | |
aggregating... | |
Done | |
Constructing graphics... | |
Hit <Return> to see next plot: | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
pltCls> ## Resize the plot window and the labels will look good. | |
pltCls> | |
pltCls> ## Not run: | |
pltCls> ##D ## For a custom plot, check the ggbio and ggplot2 packages. | |
pltCls> ##D ## Also feel free to look at the code for this function: | |
pltCls> ##D plotCluster | |
pltCls> ##D | |
pltCls> ## End(Not run) | |
pltCls> | |
pltCls> | |
pltCls> | |
There were 33 warnings (use warnings() to see them) | |
> warnings() | |
Warning messages: | |
1: In getIdeoGR(data) : | |
geom(ideogram) need valid seqlengths information for accurate mapping, | |
now use reduced information as ideogram... | |
2: In .local(x, drop.empty.ranges, ...) : | |
partial argument match of 'ignore' to 'ignore.strand' | |
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
5: `quo_expr()` is deprecated as of rlang 0.2.0. | |
Please use `quo_squash()` instead. | |
This warning is displayed once per session. | |
6: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
7: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
8: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
9: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
10: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
11: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
12: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
13: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
14: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
15: Transformation introduced infinite values in continuous y-axis | |
16: Transformation introduced infinite values in continuous y-axis | |
17: partial match of 'width' to 'widths' | |
18: partial match of 'width' to 'widths' | |
19: partial match of 'width' to 'widths' | |
20: partial match of 'width' to 'widths' | |
21: partial match of 'width' to 'widths' | |
22: partial match of 'width' to 'widths' | |
23: partial match of 'width' to 'widths' | |
24: partial match of 'width' to 'widths' | |
25: partial match of 'width' to 'widths' | |
26: partial match of 'width' to 'widths' | |
27: partial match of 'width' to 'widths' | |
28: partial match of 'width' to 'widths' | |
29: In rep(label.text.angle, len = length(grobs)) : | |
partial argument match of 'len' to 'length.out' | |
30: In rep(label.text.color, len = length(grobs)) : | |
partial argument match of 'len' to 'length.out' | |
31: In rep(label.text.cex, len = length(grobs)) : | |
partial argument match of 'len' to 'length.out' | |
32: In rep(label.bg.color, len = length(grobs)) : | |
partial argument match of 'len' to 'length.out' | |
33: In rep(label.bg.fill, len = length(grobs)) : | |
partial argument match of 'len' to 'length.out' | |
> | |
> | |
> q() | |
Save workspace image? [y/n/c]: n | |
09:31 Code $ R | |
R version 4.0.0 alpha (2020-04-07 r78176) | |
Copyright (C) 2020 The R Foundation for Statistical Computing | |
Platform: x86_64-apple-darwin17.0 (64-bit) | |
R is free software and comes with ABSOLUTELY NO WARRANTY. | |
You are welcome to redistribute it under certain conditions. | |
Type 'license()' or 'licence()' for distribution details. | |
Natural language support but running in an English locale | |
R is a collaborative project with many contributors. | |
Type 'contributors()' for more information and | |
'citation()' on how to cite R or R packages in publications. | |
Type 'demo()' for some demos, 'help()' for on-line help, or | |
'help.start()' for an HTML browser interface to help. | |
Type 'q()' to quit R. | |
Loading required package: colorout | |
> library('derfinderPlot') | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
> example('plotCluster') | |
pltCls> ## Load data | |
pltCls> library('derfinder') | |
pltCls> ## Annotate the results with bumphunter::matchGenes() | |
pltCls> library('bumphunter') | |
Loading required package: S4Vectors | |
Loading required package: stats4 | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: 'BiocGenerics' | |
The following objects are masked from 'package:parallel': | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
clusterExport, clusterMap, parApply, parCapply, parLapply, | |
parLapplyLB, parRapply, parSapply, parSapplyLB | |
The following objects are masked from 'package:stats': | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from 'package:base': | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, | |
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, | |
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, | |
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, | |
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, | |
union, unique, unsplit, which, which.max, which.min | |
Attaching package: 'S4Vectors' | |
The following object is masked from 'package:base': | |
expand.grid | |
Loading required package: IRanges | |
Loading required package: GenomeInfoDb | |
Loading required package: GenomicRanges | |
Loading required package: foreach | |
Loading required package: iterators | |
Loading required package: locfit | |
locfit 1.5-9.4 2020-03-24 | |
pltCls> library('TxDb.Hsapiens.UCSC.hg19.knownGene') | |
Loading required package: GenomicFeatures | |
Loading required package: AnnotationDbi | |
Loading required package: Biobase | |
Welcome to Bioconductor | |
Vignettes contain introductory material; view with | |
'browseVignettes()'. To cite Bioconductor, see | |
'citation("Biobase")', and for packages 'citation("pkgname")'. | |
pltCls> library('org.Hs.eg.db') | |
pltCls> genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene, | |
pltCls+ annotationPackage = 'org.Hs.eg.db') | |
Getting TSS and TSE. | |
Getting CSS and CSE. | |
Getting exons. | |
Annotating genes. | |
pltCls> annotation <- matchGenes(x = genomeRegions$regions, subject = genes) | |
pltCls> ## Make the plot | |
pltCls> plotCluster(idx=1, regions=genomeRegions$regions, annotation=annotation, | |
pltCls+ coverageInfo=genomeDataRaw$coverage, groupInfo=genomeInfo$pop, | |
pltCls+ txdb=TxDb.Hsapiens.UCSC.hg19.knownGene) | |
Parsing transcripts... | |
Parsing exons... | |
Parsing cds... | |
Parsing utrs... | |
------exons... | |
------cdss... | |
------introns... | |
------utr... | |
aggregating... | |
Done | |
Constructing graphics... | |
Hit <Return> to see next plot: | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
Coordinate system already present. Adding new coordinate system, which will replace the existing one. | |
pltCls> ## Resize the plot window and the labels will look good. | |
pltCls> | |
pltCls> ## Not run: | |
pltCls> ##D ## For a custom plot, check the ggbio and ggplot2 packages. | |
pltCls> ##D ## Also feel free to look at the code for this function: | |
pltCls> ##D plotCluster | |
pltCls> ##D | |
pltCls> ## End(Not run) | |
pltCls> | |
pltCls> | |
pltCls> | |
There were 33 warnings (use warnings() to see them) | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R version 4.0.0 alpha (2020-04-07 r78176) | |
os macOS Catalina 10.15.4 | |
system x86_64, darwin17.0 | |
ui X11 | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz America/New_York | |
date 2020-04-09 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.0.0) | |
AnnotationDbi * 1.49.1 2020-04-07 [1] Bioconductor | |
AnnotationFilter 1.11.0 2020-04-07 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) | |
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0) | |
Biobase * 2.47.3 2020-04-07 [1] Bioconductor | |
BiocFileCache 1.11.4 2020-04-07 [1] Bioconductor | |
BiocGenerics * 0.33.3 2020-04-07 [1] Bioconductor | |
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0) | |
BiocParallel 1.21.2 2020-04-07 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-07 [1] Bioconductor | |
Biostrings 2.55.7 2020-04-07 [1] Bioconductor | |
biovizBase 1.35.1 2020-04-07 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0) | |
BSgenome 1.55.4 2020-04-07 [1] Bioconductor | |
bumphunter * 1.29.0 2020-04-07 [1] Bioconductor | |
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0) | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0) | |
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0) | |
codetools 0.2-16 2018-12-24 [1] CRAN (R 4.0.0) | |
colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0) | |
DelayedArray 0.13.10 2020-04-07 [1] Bioconductor | |
derfinder * 1.21.0 2020-04-07 [1] Bioconductor | |
derfinderHelper 1.21.0 2020-04-07 [1] Bioconductor | |
derfinderPlot * 1.21.0 2020-04-07 [1] Bioconductor | |
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0) | |
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0) | |
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.0.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0) | |
doRNG 1.8.2 2020-01-27 [1] CRAN (R 4.0.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0) | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0) | |
ensembldb 2.11.3 2020-04-07 [1] Bioconductor | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0) | |
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0) | |
foreach * 1.5.0 2020-03-30 [1] CRAN (R 4.0.0) | |
foreign 0.8-77 2020-03-25 [1] CRAN (R 4.0.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.0.0) | |
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0) | |
GenomeInfoDb * 1.23.16 2020-04-07 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-08 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-04-07 [1] Bioconductor | |
GenomicFeatures * 1.39.7 2020-04-07 [1] Bioconductor | |
GenomicFiles 1.23.2 2020-04-07 [1] Bioconductor | |
GenomicRanges * 1.39.3 2020-04-07 [1] Bioconductor | |
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.0.0) | |
ggbio 1.35.1 2020-04-07 [1] Bioconductor | |
ggplot2 3.3.0 2020-03-05 [1] CRAN (R 4.0.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0) | |
graph 1.65.2 2020-04-07 [1] Bioconductor | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.0.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.0.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0) | |
IRanges * 2.21.8 2020-04-07 [1] Bioconductor | |
iterators * 1.0.12 2019-07-26 [1] CRAN (R 4.0.0) | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0) | |
labeling 0.3 2014-08-23 [1] CRAN (R 4.0.0) | |
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.0) | |
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0) | |
limma 3.43.5 2020-04-07 [1] Bioconductor | |
locfit * 1.5-9.4 2020-03-25 [1] CRAN (R 4.0.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0) | |
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0) | |
nnet 7.3-13 2020-02-25 [1] CRAN (R 4.0.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0) | |
org.Hs.eg.db * 3.10.0 2020-04-08 [1] Bioconductor | |
OrganismDbi 1.29.1 2020-04-07 [1] Bioconductor | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.0.0) | |
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0) | |
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0) | |
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0) | |
ProtGenerics 1.19.3 2020-04-07 [1] Bioconductor | |
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0) | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.0.0) | |
qvalue 2.19.0 2020-04-07 [1] Bioconductor | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0) | |
RBGL 1.63.1 2020-04-07 [1] Bioconductor | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0) | |
Rcpp 1.0.4.6 2020-04-08 [1] Github (RcppCore/Rcpp@a831639) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.0.0) | |
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0) | |
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.0.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.0.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0) | |
rngtools 1.5 2020-01-23 [1] CRAN (R 4.0.0) | |
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.0) | |
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0) | |
Rsamtools 2.3.7 2020-04-07 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0) | |
rtracklayer 1.47.0 2020-04-07 [1] Bioconductor | |
S4Vectors * 0.25.15 2020-04-07 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0) | |
SummarizedExperiment 1.17.5 2020-04-07 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [1] CRAN (R 4.0.0) | |
testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.0.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0) | |
TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2020-04-08 [1] Bioconductor | |
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.0.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.0.0) | |
XVector 0.27.2 2020-04-07 [1] Bioconductor | |
zlibbioc 1.33.1 2020-04-07 [1] Bioconductor | |
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library |
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### ~/.Rprofile content that applies here: | |
### (relates to the warnings shown and the session info) | |
options( | |
warnPartialMatchArgs = TRUE, | |
warnPartialMatchDollar = TRUE, | |
warnPartialMatchAttr = TRUE | |
) | |
if (interactive()) { | |
suppressMessages(require(devtools)) | |
suppressMessages(require(usethis)) | |
suppressMessages(require(testthat)) | |
suppressMessages(require(colorout)) | |
} | |
$ R | |
R version 4.0.0 alpha (2020-04-07 r78176) | |
Copyright (C) 2020 The R Foundation for Statistical Computing | |
Platform: x86_64-apple-darwin17.0 (64-bit) | |
R is free software and comes with ABSOLUTELY NO WARRANTY. | |
You are welcome to redistribute it under certain conditions. | |
Type 'license()' or 'licence()' for distribution details. | |
Natural language support but running in an English locale | |
R is a collaborative project with many contributors. | |
Type 'contributors()' for more information and | |
'citation()' on how to cite R or R packages in publications. | |
Type 'demo()' for some demos, 'help()' for on-line help, or | |
'help.start()' for an HTML browser interface to help. | |
Type 'q()' to quit R. | |
Loading required package: colorout | |
> library('ggbio') | |
Loading required package: BiocGenerics | |
Loading required package: parallel | |
Attaching package: ‘BiocGenerics’ | |
The following objects are masked from ‘package:parallel’: | |
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, | |
clusterExport, clusterMap, parApply, parCapply, parLapply, | |
parLapplyLB, parRapply, parSapply, parSapplyLB | |
The following objects are masked from ‘package:stats’: | |
IQR, mad, sd, var, xtabs | |
The following objects are masked from ‘package:base’: | |
anyDuplicated, append, as.data.frame, basename, cbind, colnames, | |
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, | |
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, | |
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, | |
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, | |
union, unique, unsplit, which, which.max, which.min | |
Loading required package: ggplot2 | |
Registered S3 method overwritten by 'GGally': | |
method from | |
+.gg ggplot2 | |
Need specific help about ggbio? try mailing | |
the maintainer or visit http://tengfei.github.com/ggbio/ | |
Attaching package: 'ggbio' | |
The following objects are masked from 'package:ggplot2': | |
geom_bar, geom_rect, geom_segment, ggsave, stat_bin, stat_identity, | |
xlim | |
> data(hg19IdeogramCyto, package = 'biovizBase') | |
> p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21') | |
Warning messages: | |
1: In getIdeoGR(data) : | |
geom(ideogram) need valid seqlengths information for accurate mapping, | |
now use reduced information as ideogram... | |
2: In .local(x, drop.empty.ranges, ...) : | |
partial argument match of 'ignore' to 'ignore.strand' | |
3: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
4: `panel.margin` is deprecated. Please use `panel.spacing` property instead | |
> tracks(p.ideo) | |
There were 11 warnings (use warnings() to see them) | |
> | |
> validObject(hg19IdeogramCyto) | |
Error in validObject(hg19IdeogramCyto) : | |
invalid class "GRanges" object: slots in class definition but not in object: "elementType" | |
> | |
> options(width = 120) | |
> sessioninfo::session_info() | |
─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────── | |
setting value | |
version R version 4.0.0 alpha (2020-04-07 r78176) | |
os macOS Catalina 10.15.4 | |
system x86_64, darwin17.0 | |
ui X11 | |
language (EN) | |
collate en_US.UTF-8 | |
ctype en_US.UTF-8 | |
tz America/New_York | |
date 2020-04-09 | |
─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────── | |
package * version date lib source | |
acepack 1.4.1 2016-10-29 [1] CRAN (R 4.0.0) | |
AnnotationDbi 1.49.1 2020-04-07 [1] Bioconductor | |
AnnotationFilter 1.11.0 2020-04-07 [1] Bioconductor | |
askpass 1.1 2019-01-13 [1] CRAN (R 4.0.0) | |
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.0) | |
backports 1.1.6 2020-04-05 [1] CRAN (R 4.0.0) | |
base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.0.0) | |
Biobase 2.47.3 2020-04-07 [1] Bioconductor | |
BiocFileCache 1.11.4 2020-04-07 [1] Bioconductor | |
BiocGenerics * 0.33.3 2020-04-07 [1] Bioconductor | |
BiocManager 1.30.10 2019-11-16 [1] CRAN (R 4.0.0) | |
BiocParallel 1.21.2 2020-04-07 [1] Bioconductor | |
biomaRt 2.43.5 2020-04-07 [1] Bioconductor | |
Biostrings 2.55.7 2020-04-07 [1] Bioconductor | |
biovizBase 1.35.1 2020-04-07 [1] Bioconductor | |
bit 1.1-15.2 2020-02-10 [1] CRAN (R 4.0.0) | |
bit64 0.9-7 2017-05-08 [1] CRAN (R 4.0.0) | |
bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0) | |
blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.0) | |
BSgenome 1.55.4 2020-04-07 [1] Bioconductor | |
callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.0) | |
checkmate 2.0.0 2020-02-06 [1] CRAN (R 4.0.0) | |
cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.0) | |
cluster 2.1.0 2019-06-19 [1] CRAN (R 4.0.0) | |
colorout * 1.2-2 2020-03-16 [1] Github (jalvesaq/colorout@726d681) | |
colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.0) | |
crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.0) | |
curl 4.3 2019-12-02 [1] CRAN (R 4.0.0) | |
data.table 1.12.8 2019-12-09 [1] CRAN (R 4.0.0) | |
DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.0) | |
dbplyr 1.4.2 2019-06-17 [1] CRAN (R 4.0.0) | |
DelayedArray 0.13.10 2020-04-07 [1] Bioconductor | |
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.0) | |
devtools * 2.2.2 2020-02-17 [1] CRAN (R 4.0.0) | |
dichromat 2.0-0 2013-01-24 [1] CRAN (R 4.0.0) | |
digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.0) | |
dplyr 0.8.5 2020-03-07 [1] CRAN (R 4.0.0) | |
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 4.0.0) | |
ensembldb 2.11.3 2020-04-07 [1] Bioconductor | |
fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.0) | |
farver 2.0.3 2020-01-16 [1] CRAN (R 4.0.0) | |
foreign 0.8-77 2020-03-25 [1] CRAN (R 4.0.0) | |
Formula 1.2-3 2018-05-03 [1] CRAN (R 4.0.0) | |
fs 1.4.1 2020-04-04 [1] CRAN (R 4.0.0) | |
GenomeInfoDb 1.23.16 2020-04-07 [1] Bioconductor | |
GenomeInfoDbData 1.2.2 2020-04-08 [1] Bioconductor | |
GenomicAlignments 1.23.2 2020-04-07 [1] Bioconductor | |
GenomicFeatures 1.39.7 2020-04-07 [1] Bioconductor | |
GenomicRanges 1.39.3 2020-04-07 [1] Bioconductor | |
GGally 1.5.0 2020-03-25 [1] CRAN (R 4.0.0) | |
ggbio * 1.35.1 2020-04-07 [1] Bioconductor | |
ggplot2 * 3.3.0 2020-03-05 [1] CRAN (R 4.0.0) | |
glue 1.4.0 2020-04-03 [1] CRAN (R 4.0.0) | |
graph 1.65.2 2020-04-07 [1] Bioconductor | |
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.0.0) | |
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.0) | |
Hmisc 4.4-0 2020-03-23 [1] CRAN (R 4.0.0) | |
hms 0.5.3 2020-01-08 [1] CRAN (R 4.0.0) | |
htmlTable 1.13.3 2019-12-04 [1] CRAN (R 4.0.0) | |
htmltools 0.4.0 2019-10-04 [1] CRAN (R 4.0.0) | |
htmlwidgets 1.5.1 2019-10-08 [1] CRAN (R 4.0.0) | |
httr 1.4.1 2019-08-05 [1] CRAN (R 4.0.0) | |
IRanges 2.21.8 2020-04-07 [1] Bioconductor | |
jpeg 0.1-8.1 2019-10-24 [1] CRAN (R 4.0.0) | |
knitr 1.28 2020-02-06 [1] CRAN (R 4.0.0) | |
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.0) | |
latticeExtra 0.6-29 2019-12-19 [1] CRAN (R 4.0.0) | |
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.0) | |
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.0) | |
magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.0) | |
Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.0) | |
matrixStats 0.56.0 2020-03-13 [1] CRAN (R 4.0.0) | |
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.0) | |
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.0) | |
nnet 7.3-13 2020-02-25 [1] CRAN (R 4.0.0) | |
openssl 1.4.1 2019-07-18 [1] CRAN (R 4.0.0) | |
OrganismDbi 1.29.1 2020-04-07 [1] Bioconductor | |
pillar 1.4.3 2019-12-20 [1] CRAN (R 4.0.0) | |
pkgbuild 1.0.6 2019-10-09 [1] CRAN (R 4.0.0) | |
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.0) | |
pkgload 1.0.2 2018-10-29 [1] CRAN (R 4.0.0) | |
plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.0) | |
png 0.1-7 2013-12-03 [1] CRAN (R 4.0.0) | |
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.0) | |
processx 3.4.2 2020-02-09 [1] CRAN (R 4.0.0) | |
progress 1.2.2 2019-05-16 [1] CRAN (R 4.0.0) | |
ProtGenerics 1.19.3 2020-04-07 [1] Bioconductor | |
ps 1.3.2 2020-02-13 [1] CRAN (R 4.0.0) | |
purrr 0.3.3 2019-10-18 [1] CRAN (R 4.0.0) | |
R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.0) | |
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.0) | |
RBGL 1.63.1 2020-04-07 [1] Bioconductor | |
RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 4.0.0) | |
Rcpp 1.0.4.6 2020-04-08 [1] Github (RcppCore/Rcpp@a831639) | |
RCurl 1.98-1.1 2020-01-19 [1] CRAN (R 4.0.0) | |
remotes 2.1.1 2020-02-15 [1] CRAN (R 4.0.0) | |
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.0.0) | |
reshape2 1.4.3 2017-12-11 [1] CRAN (R 4.0.0) | |
rlang 0.4.5 2020-03-01 [1] CRAN (R 4.0.0) | |
rpart 4.1-15 2019-04-12 [1] CRAN (R 4.0.0) | |
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.0) | |
Rsamtools 2.3.7 2020-04-07 [1] Bioconductor | |
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 4.0.0) | |
rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.0) | |
rtracklayer 1.47.0 2020-04-07 [1] Bioconductor | |
S4Vectors 0.25.15 2020-04-07 [1] Bioconductor | |
scales 1.1.0 2019-11-18 [1] CRAN (R 4.0.0) | |
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.0) | |
stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0) | |
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.0) | |
SummarizedExperiment 1.17.5 2020-04-07 [1] Bioconductor | |
survival 3.1-11 2020-03-07 [1] CRAN (R 4.0.0) | |
testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.0) | |
tibble 3.0.0 2020-03-30 [1] CRAN (R 4.0.0) | |
tidyselect 1.0.0 2020-01-27 [1] CRAN (R 4.0.0) | |
usethis * 1.5.1 2019-07-04 [1] CRAN (R 4.0.0) | |
VariantAnnotation 1.33.2 2020-03-18 [1] Bioconductor | |
vctrs 0.2.4 2020-03-10 [1] CRAN (R 4.0.0) | |
withr 2.1.2 2018-03-15 [1] CRAN (R 4.0.0) | |
xfun 0.12 2020-01-13 [1] CRAN (R 4.0.0) | |
XML 3.99-0.3 2020-01-20 [1] CRAN (R 4.0.0) | |
XVector 0.27.2 2020-04-07 [1] Bioconductor | |
zlibbioc 1.33.1 2020-04-07 [1] Bioconductor | |
[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library |
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library('derfinderPlot') | |
example('plotCluster') | |
options(width = 120) | |
sessioninfo::session_info() |
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library('ggbio') | |
data(hg19IdeogramCyto, package = 'biovizBase') | |
p.ideo <- plotIdeogram(hg19IdeogramCyto, 'chr21') | |
tracks(p.ideo) | |
validObject(hg19IdeogramCyto) | |
options(width = 120) | |
sessioninfo::session_info() |
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