jokergoo

x = sessionInfo()

base_pkgs = x$basePkgs
other_pkgs = sapply(x$otherPkgs, function(x)x$Package)
loaded_pkgs = sapply(x$loadedOnly, function(x)x$Package)


db = reformat_db(installed.packages())

jokergoo

library(COVID19)
library(ComplexHeatmap)
library(circlize)
library(spiralize)
library(RColorBrewer)
library(shiny)
library(lubridate)

env = new.env()

jokergoo

x = sort(runif(20))

df1 = data.frame(x1 = x[1:20 %% 2 == 0], x2 = x[1:20 %% 2 == 1])
df1 = cbind(gene = "A", df1)

x = sort(runif(10, max = 0.5))

df2 = data.frame(x1 = x[1:10 %% 2 == 0], x2 = x[1:10 %% 2 == 1])

jokergoo

library(grid)


grid.newpage()
pushViewport(viewport())
str = "Hfgj"
gb = textGrob(str, 0.2, 0.5, gp = gpar(fontsize = 60, fontfamily = "mono"))
grid.draw(gb)
grid.points(0.2, 0.5, pch = 16,  gp = gpar(col = "red"))
grid.rect(0.2, 0.5, width = grobWidth(gb), height = grobHeight(gb), gp = gpar(col = "black"))

jokergoo

library(rvest)
library(jsonlite)
downloads_from_conda = function(pkg) {
	x = read_html(paste0("https://anaconda.org/search?q=r-", pkg))
	tb = html_nodes(x, "table") %>% html_table()
	if(length(tb) > 0) {
		tb = tb[[1]]
		sum(tb[, 2])
	} else {
		0

jokergoo

rect3D = function(x, y, w, h, l, theta = 60, default.units = "npc", fill = "white", col = "black") {

	if(!is.unit(x)) x = unit(x, default.units)
	if(!is.unit(y)) y = unit(y, default.units)
	if(!is.unit(w)) w = unit(w, default.units)
	if(!is.unit(h)) h = unit(h, default.units)
	if(!is.unit(l)) l = unit(l, default.units)

	x1 = x - w*0.5
	x2 = x + w*0.5

jokergoo

library(GenomicRanges)
library(HilbertCurve)
library(ComplexHeatmap)
library(InteractiveComplexHeatmap)
library(GetoptLong)

file_list = c(
	"IDH_DMV" = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121721/suppl/GSE121721_IDH_methylation_features_DMV.bed.gz",
	"IDH_LMR" = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121721/suppl/GSE121721_IDH_methylation_features_LMR.bed.gz",
	"IDH_PMD" = "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE121nnn/GSE121721/suppl/GSE121721_IDH_methylation_features_PMD.bed.gz",

jokergoo

library(rtracklayer)
library(circlize)
library(EnrichedHeatmap)


viz_lift_over = function(from = "hg19", to = "hg38", 
	from_chromosomes = NULL, to_chromosomes = NULL,
	window_size = 5000, links_to_sample = 10000) {

	to2 = to

jokergoo

library(circlize)
library(ComplexHeatmap)

mat = matrix(runif(100), 10)

col_fun = colorRamp2(c(0, 0.1, 1), c("blue", "white", "red"))

Heatmap(mat, col = col_fun, cell_fun = function(j, i, x, y, w, h, fill) {
	if(mat[i, j] < 0.1) {

jokergoo

library(matrixStats)
library(genefilter)

gene_level = function(mat, condition, method = "tvalue", transform = "none", 
    binarize = function(x) x) {
        
    le = levels(condition)
    l_group1 = condition == le[1]
    l_group2 = !l_group1