slowkow

# ~/.Rprofile

ggplot2_discrete_pals <- list(
  "tol" = c(
    "#77AADD", "#EE8866", "#EEDD88", "#FFAABB", "#99DDFF", "#44BB99",
    "#BBCC33", "#AAAA00"
  ),
  "okabe" = c(
    "#E69F00", "#56B4E9", "#009E73", "#F5C710", "#0072B2", "#D55E00",
    "#CC79A7", "#999999", "#000000"

slowkow

# find_correlated_genes.R
# 2024-03-12
# Kamil Slowikowski

library(arrow) # install.packages("arrow")

# Download correlation from ARCHS4 <https://maayanlab.cloud/archs4/download.html>
# wget https://s3.amazonaws.com/mssm-data/human_correlation_archs4.f

# The file is large:

slowkow

How to update figure references in Word

Add a new caption in the Figure Legends section of your manuscript:

• In the menu bar, click Insert > Caption...
• Type a name like "My great data" — you can always change it later.
• Click OK

slowkow

Make a montage of circle-cropped photos

Here are the source files, the masked output folder, and the montage.png output file:

Here are the images in the masked output folder:

slowkow

library(data.table)
library(glue)
library(rgl)

# https://github.com/google/palette.js/blob/master/palette.js
mpn65 <- c(
  '#ff0029', '#377eb8', '#66a61e', '#984ea3', '#00d2d5', '#ff7f00', '#af8d00',
  '#7f80cd', '#b3e900', '#c42e60', '#a65628', '#f781bf', '#8dd3c7', '#bebada',
  '#fb8072', '#80b1d3', '#fdb462', '#fccde5', '#bc80bd', '#ffed6f', '#c4eaff',
  '#cf8c00', '#1b9e77', '#d95f02', '#e7298a', '#e6ab02', '#a6761d', '#0097ff',

slowkow

#!/usr/bin/bash
#$ -N MY_JOB_NAME
#$ -o /path/on/broad/server/
#$ -e /path/on/broad/server/
#$ -cwd
#$ -j y
#$ -l h_rt=12:00:00
#$ -pe smp 8 -R y -binding linear:8
#$ -l h_vmem=2G
#

slowkow

library(uwot)
library(scattermore)
library(foreach)
library(doParallel)
library(data.table)
library(ggplot2)
library(scales)
library(glue)

# This code snippet assumes we have these objects:

slowkow

#!/usr/bin/env python3
# pay-water-bill.py
# 2021-05-02

"""
Pay your water bill in Baltimore City
=====================================

Steps:

slowkow

#!/usr/bin/env python
"""
montage.py
2020-12-23
Kamil Slowikowski

Usage
-----

Write montage.png from a list of PDF files, each panel 500px wide:

slowkow

#!/usr/bin/env Rscript
# rsa-example.R
#
# Inspired by Alex Van de Sande
# https://twitter.com/avsa/status/1318672796415819776

last_digit <- function(x) {
  x_char <- as.character(x)
  as.numeric(substr(x_char, nchar(x_char), nchar(x_char)))
}