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library(ComplexHeatmap) | |
set.seed(123) | |
mat = matrix(rnorm(100), 10) | |
rownames(mat) = letters[1:10] | |
ht = Heatmap(mat, | |
column_title = gt_render("Some <span style='color:blue'>blue text **in bold.**</span><br>And *italics text.*<br>And some <span style='font-size:18pt; color:black'>large</span> text.", | |
r = unit(2, "pt"), | |
padding = unit(c(2, 2, 2, 2), "pt")), | |
column_title_gp = gpar(box_fill = "orange"), |
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library(GenomicInteractions) | |
data(hic_example_data) | |
hic_example_data = as.data.frame(hic_example_data) | |
hic_example_data = hic_example_data[hic_example_data$seqnames1 == hic_example_data$seqnames2, ] | |
gr1 = hic_example_data[, c("seqnames1", "start1", "end1")] | |
colnames(gr1) = c("chr", "start", "end") |
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mat = matrix(0, nrow = 10, ncol = 27) | |
mat[2, c(1, 2, 3, 13, 14, 15, 17, 23, 25)] = 1 | |
mat[3, c(1, 5, 6, 7, 9, 10, 11, 13, 15, 17, 19, 20, 21, 23, 24, 25)] = 1 | |
mat[4, c(1, 5, 7, 9, 10, 11, 13, 14, 17, 19, 21, 24)] = 1 | |
mat[5, c(1, 2, 3, 5, 6, 7, 9, 11, 13, 17, 19, 20, 23, 25)] = 1 | |
mat[7, c(1, 3, 14, 25, 26, 27)] = 1 | |
mat[8, c(1, 3, 5, 6, 7, 10, 11, 13, 14, 15, 17, 18, 19, 21, 22, 23, 25, 27)] = 1 |
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giggle_dir = "/icgc/dkfzlsdf/analysis/B080/guz/giggle_test/giggle" | |
giggle_data_dir = "/icgc/dkfzlsdf/analysis/hipo/hipo_016/analysis/WGBS_final_cohort/giggle_data" | |
temp_dir = "/icgc/dkfzlsdf/analysis/hipo/hipo_016/analysis/WGBS_final_cohort/temp" | |
library(GetoptLong) | |
build_giggle_index = function(gr_list, name = "anno") { | |
system(qq("mkdir @{giggle_data_dir}/@{name}")) | |
# write as bed files | |
for(nm in names(gr_list)) { | |
qqcat("writing @{nm}.bed\n") |
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#!c:/perl/bin/perl -w | |
use strict; | |
use LWP::Simple; | |
use CGI; | |
my $package = param("package") | |
if($package eq "ComplexHeatmap" or | |
$package eq "EnrichedHeatmap" or |
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Path of SRA files: | |
http://sra-download.ncbi.nlm.nih.gov/srapub/SRR\\d+ |
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var unread = new Array(); | |
var checked = new Array(); | |
var from = new Array(); | |
var subject = new Array(); | |
var rows = new Array(); | |
load_all = function() { | |
rows = document.getElementsByClassName("lvm")[0].lastChild.childNodes; |
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is_abs_unit <- function(x) UseMethod("is_abs_unit") | |
is_abs_unit.unit = function(x) { | |
unit = attr(x, "valid.unit") | |
if(unit %in% c(1:4, 7:24)) { | |
return(TRUE) | |
} else { | |
return(FALSE) | |
} |
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set_module = function(module) { | |
assign("__module__", module, envir = parent.frame()) | |
} | |
load_module = function(file) { | |
e = new.env() | |
source(file, local = e, verbose = FALSE) | |
module = get("__module__", envir = e) | |
rm(e) |
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bedtools = function(cmd, envir = parent.frame()) { | |
gr = gsub("^.*@\\{(.*?)\\}.*$", "\\1", cmd) | |
gr = get(gr, envir = envir) | |
file = tempfile(fileext = ".bed") | |
write.table(gr, file = file, sep = "\t", quote = FALSE, row.names = FALSE, col.names = FALSE) | |
cmd = gsub("@\\{.*?\\}", file, cmd) | |
try(tb <- read.table(pipe(cmd), stringsAsFactors = FALSE)) | |
file.remove(file) | |
return(tb) | |
} |