jokergoo

#!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 

jokergoo

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")

jokergoo

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

jokergoo

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")

jokergoo

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"),

jokergoo

library(grid)
word_cloud_grob = function(text, fontsize, 
	line_space = unit(4, "pt"), word_space = unit(4, "pt"), max_width = unit(80, "mm"), 
	col = function(fs) circlize::rand_color(length(fs), luminosity = "dark"),
	test = FALSE) { # width in mm

	if(length(text) != length(fontsize)) {
		stop("`text` and `fontsize` should the same length.")
	}
	

jokergoo

set.seed(123)
m = matrix(rnorm(100*10), nrow = 100)

# you should clustr the columns before making the heatmap because the column
# ordering will be used in `panel.fun`
column_hclust = hclust(dist(t(m)))

subgroup = sample(letters[1:3], 100, replace = TRUE, prob = c(1, 5, 10))
rg = range(m)

jokergoo

library(circlize)
seed_color = c("1-3" = 2,
               "4-6" = 3,
               "7-9" = 4,
               "10-12" = 5,
               "13-16" = 6,
               "(Missing)" = "grey")
round_name = c("Champoin",
               "Runner-up",
               "Final Four",

jokergoo

library(circlize)

par(mfrow = c(2, 2))

circos.initialize(c("a"), xlim = c(0, 1))
circos.track(ylim = c(0, 1), track.height = 0.7, bg.border = NA, 
	panel.fun = function(x, y) {
	circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[1], 2), col = "#CCCCCC")
	circos.lines(CELL_META$cell.xlim, rep(CELL_META$cell.ylim[2], 2), col = "#CCCCCC")
	x0 = runif(1000)

jokergoo

gsub_eval = function(pattern, replacement, x, ignore.case = FALSE, perl = FALSE,
    fixed = FALSE, useBytes = FALSE, envir = parent.frame()) {
    txt = gsub(
        pattern = pattern, 
        replacement = replacement, 
        x = x, 
        ignore.case = ignore.case, 
        perl = perl,
        fixed = fixed, 
        useBytes = useBytes