diazdc’s gists

diazdc / keep_R_alive.R

Created August 7, 2020 21:00

Launches background process from R so you don't get disconnected from an idle session if you

parallel::mcparallel(system('ping -i 600 www.google.com'))

diazdc / conda_install_all.sh

Created February 27, 2020 16:25

Bash script to install to all conda environments

	# from https://stackoverflow.com/questions/24117449/install-a-package-into-multiple-all-conda-environments
	conda env list \| cut -d" " -f1 \| tail -n+4 \| xargs -L 1 conda install YOUR_PACKAGE -n

diazdc / OneMonokai_update.json

Created February 24, 2020 23:23

Modded colors for the vscode OneMonokai theme

	{
	"$schema": "vscode://schemas/color-theme",
	"type": "dark",
	"colors": {
	"activityBar.background": "#2f333d",
	"activityBar.foreground": "#d7dae0",
	"activityBarBadge.background": "#528bff",
	"activityBarBadge.foreground": "#f8fafd",
	"button.background": "#528bff",
	"diffEditor.insertedTextBackground": "#00809b33",

diazdc / git_show.sh

Created February 20, 2020 23:13

Generate file from old git commit or branch

	# HEAD~1 is a single commit back, HEAD~2 is two..
	# Don't forget to write the full path
	git show HEAD:all_regeneration_datasets_Sungmin/app.R

diazdc / env_var_sizes.R

Created January 8, 2020 19:04

Print R environment variable sizes

	for (i in seq_along(ls())) {
	objects <- ls()
	obj_size <- object.size(get(objects[i]))
	cat("\n")
	print(objects[i])

	if (obj_size > 1 * 10^9) {
	print(obj_size, units = "GB")
	} else if (obj_size > 1 * 10^6) {
	print(obj_size, units = "MB")

diazdc / SeuratObjSize.R

Created January 7, 2020 23:48

Print Seurat object slot sizes in MB

	SeuratObjSize <- function(seurat_obj) {
	all_slots <- slotNames(seurat_obj)

	for (i in seq_along(all_slots)) {
	obj_size <- object.size(slot(seurat_obj, all_slots[i]))

	print(all_slots[i])
	print(obj_size, units = "MB")
	cat("\n")
	}

diazdc / conda_PS1.sh

Last active November 13, 2019 16:31

Colored conda environment prompt with user name

	# must overide default conda PS1 with "conda config --set changeps1 False' first
	PS1='(\[\e[0;32m\]$(basename "$CONDA_DEFAULT_ENV")\[\e[m\]) \u\[\e[0;90m\]@\[\e[m\]\h ';

diazdc / mcFindMarkers.R

Last active January 4, 2025 11:08

Multicore solution for Seurat FindAllMarkers()

	n_clust <- 1:(max(as.numeric(Idents(seurat_obj))))
	mcFindMarkers <- function(i){
	ident1 <- i
	ident2 <- n_clust[n_clust != i]
	table <- FindMarkers(seurat_obj,
	ident.1 = ident1, ident.2 = ident2, only.pos = TRUE)
	table$Gene.name.uniq <- rownames(table)
	table$cluster <- rep(i, nrow(table))
	return(table)
	}

diazdc / gg_color_hue.R

Created September 11, 2019 14:07

ggplot color generator

diazdc / objectSize.R

Last active April 18, 2019 15:43

	# Get size of each slot in Seurat object
	objectSize <- function(seurat_obj) {
	slots <- slotNames(seurat_obj)
	for (i in 1:length(slots)) {
	print(paste0(slots[i], " - ", class(slot(seurat_obj, slots[i]))))
	print(object.size(slot(seurat_obj, slots[i])), units = "auto")
	}
	}