Vince Carey vjcitn
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| <?xml version="1.0"?> | |
| <Ontology xmlns="http://www.w3.org/2002/07/owl#" | |
| xml:base="http://www.semanticweb.org/vincent/ontologies/2024/7/untitled-ontology-10" | |
| xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" | |
| xmlns:xml="http://www.w3.org/XML/1998/namespace" | |
| xmlns:xsd="http://www.w3.org/2001/XMLSchema#" | |
| xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" | |
| ontologyIRI="http://www.semanticweb.org/vincent/ontologies/2024/7/untitled-ontology-10"> | |
| <Prefix name="" IRI="http://www.semanticweb.org/vincent/ontologies/2024/7/untitled-ontology-10/"/> | |
| <Prefix name="owl" IRI="http://www.w3.org/2002/07/owl#"/> |
vjcitn
/ install_py_events.txt
Created
October 23, 2024 21:29
log of reticulate::install_python events
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| > reticulate::install_python(version="3.12") | |
| trying URL 'https://github.com/pyenv/pyenv-installer/raw/master/bin/pyenv-installer' | |
| Content type 'text/plain; charset=utf-8' length 2827 bytes | |
| ================================================== | |
| downloaded 2827 bytes | |
| Installing pyenv ... | |
| Cloning into '/home/stvjc/.local/share/r-reticulate/pyenv'... | |
| remote: Enumerating objects: 1289, done. | |
| remote: Counting objects: 100% (1289/1289), done. |
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| #' from a MAF instance create a key with ref, alt and positional information, | |
| #' return in a data.frame with key and gene symbol | |
| #' @param mafinst instance of S4 class MAF from maftools | |
| #' @param altfield character(1) name of field to use for mutation substitution | |
| #' @param donorfield character(1) name of field to use for donor | |
| #' @param uniprot_ok character() or NULL, defaults to NULL, if non-NULL, data to be returned will | |
| #' only include records with UNIPROT id matching an element in this vector | |
| #' @export | |
| maf2key = function(mafinst, altfield="Tumor_Seq_Allele2", donorfield="Tumor_Sample_Barcode", |
vjcitn
/ curlminitest.Rmd
Created
October 11, 2024 11:55
triggers segfault on ubuntu 24.04 under R 4.4.1, when compiled with rmarkdown::render
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| --- | |
| title: "Triggers a curl/httr segfault during R CMD build" | |
| author: Hervé Pagès | |
| output: | |
| BiocStyle::html_document: | |
| toc: true | |
| toc_depth: 2 | |
| vignette: > | |
| %\VignetteEngine{knitr::rmarkdown} | |
| %\VignetteEncoding{UTF-8} |
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| > sessionInfo() | |
| R version 4.4.1 Patched (2024-09-30 r87215) | |
| Platform: x86_64-pc-linux-gnu | |
| Running under: Ubuntu 24.04.1 LTS | |
| Matrix products: default | |
| BLAS: /usr/local/lib/R/lib/libRblas.so | |
| LAPACK: /usr/local/lib/R/lib/libRlapack.so; LAPACK version 3.12.0 | |
| locale: |
vjcitn
/ intel_mac_log.txt
Created
October 11, 2024 10:56
hard to trigger error first seen in ubuntu 24.04, now similar on intel mac
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| ############################################################################## | |
| ############################################################################## | |
| ### | |
| ### Running command: | |
| ### | |
| ### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data BiocFileCache | |
| ### | |
| ############################################################################## | |
| ############################################################################## |
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| library(shiny) | |
| library(xenLite) | |
| library(SpatialExperiment) | |
| what = "LUAD" | |
| ui = fluidPage( | |
| sidebarLayout( | |
| sidebarPanel( | |
| uiOutput("topbox"), |
vjcitn
/ r-dev.noload.txt
Created
September 19, 2024 02:06
error with attempt to install impute from bioc.r-universe.dev
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| setup: | |
| > options(repos=c(BioCsoft="https://bioc.r-universe.dev", CRAN="https://cloud.r-project.org")) | |
| > getOption("repos") | |
| BioCsoft CRAN | |
| "https://bioc.r-universe.dev" "https://cloud.r-project.org" | |
| > install.packages("impute") | |
| Installing package into ‘/Users/papa/Library/R/arm64/4.4/library’ |
vjcitn
/ ggplot_seg.R
Created
September 1, 2024 21:06
code that uses ggplot and some cell-level summaries on XenSPEP/XenSCE
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| library(plotly) | |
| library(ggplot2) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| print.xen_ggprep = function(x, ...) { | |
| cat(sprintf("xen_ggprep instance for %d cells with %d cell boundary vertices.\n", ncol(x$sampd), nrow(x$bounds))) | |
| } | |
| ggprep_seg = function(xsce, xlim=c(5800,6200), ylim=c(6300, 6700), show_tx=TRUE) { |
vjcitn
/ plotly_seg.R
Created
August 31, 2024 17:05
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| library(plotly) | |
| library(ggplot2) | |
| library(XenSCE) | |
| if (!exists("gbm")) load("gbm.rda") | |
| plotly_seg = function(xsce, xlim=c(5800,6000), ylim=c(6300, 6500), show_tx=TRUE) { | |
| bounds = getCellBoundaries(xsce) | |
| bounds = bounds[bounds$vertex_x > xlim[1] & | |
| bounds$vertex_x < xlim[2] & bounds$vertex_y > ylim[1] & bounds$vertex_y < ylim[2],] | |
| c4 <- as.data.frame(bounds) | |
| #ggplot(c4, aes(x=vertex_x, y=vertex_y, group=cell_id)) + geom_path() -> pas |
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