alanocallaghan

Sublime Text 2 – Useful Shortcuts (PC)

Loosely ordered with the commands I use most towards the top. Sublime also offer full documentation.

Editing

Ctrl+C	copy current line (if no selection)
Ctrl+X	cut current line (if no selection)
Ctrl+⇧+K	delete line
Ctrl+↩	insert line after

alanocallaghan

############################################
#  Syntax highlighting for R               #
#  by Stephen Haptonstahl                  #
#  March 15, 2009                          #
#  http://srh.ucdavis.edu/drupal/node/20   #
#  edited by Mike Miller                   #
#  Placed on GitHub by Alan O'Callaghan    #
#  (could no longer find the original)      #
############################################

alanocallaghan

library("ggplot2")
library("usmap")
library("httr")
library("readxl")

# Read data
GET("https://query.data.world/s/pth2w34nwc6uhg7mmvr7n56257y2gw", write_disk(tf <- tempfile(fileext = ".xlsx")))
pets <- read_excel(tf)

pets <- pets[!colnames(pets) %in% "X"]

alanocallaghan

library("scRNAseq")
library("scater")
library("scran")
library("flexmix")
library("mixtools")
library("viridis")
library("annotables")
theme_set(theme_bw())

sce <- ZeiselBrainData()

alanocallaghan

A catalogue of the bugs that have caused me not insignificant amounts of pain

R

• Dropping attributes

  matrix[, 1, drop=FALSE]

• Autocompletion for thee but not for me

alanocallaghan

# R port of Dmitry Kobak's excellent PCA animations.
# See https://gist.github.com/anonymous/7d888663c6ec679ea65428715b99bfdd
# for matlab/octave code
dir.create("gif", showWarnings = FALSE)
set.seed(42)

X <- matrix(rnorm(200), ncol = 2)
X <- X %*% chol(matrix(c(1, 0.6, 0.6, 0.6), ncol = 2, byrow = TRUE))
X <- apply(X, 2, function(col) col - mean(col))

alanocallaghan

library(utils)
for (pkg in rownames(installed.packages(priority="base"))) library(pkg, character.only=TRUE)

pkgs <- c(
    "NHANES",
    "RNHANES",
    "ggplot2",
    "jtools",
    "interactions",
    "patchwork",

alanocallaghan

#!/usr/bin/env bash

set -eu
if [ -f ~/miniconda3/etc/profile.d/conda.sh ]; then
    [ -z "${CONDA_EXE}" ] && echo "Error, missing \$CONDA_EXE !" && exit 1
    CONDA_BASE=$(${CONDA_EXE} info --base)
    ADDR2LINE=""
    source $CONDA_BASE/etc/profile.d/conda.sh
    conda activate $1 || exit 1
fi

alanocallaghan

## using natbib
## when finished adding refs, run
bibexport --nosave -o [LOCAL_BIB_FILE] main.aux
## then switch the \bibliography command from the central file to the local one, ie change
# % \bibliography{[CENTRAL_BIB_FILE]}
# % \bibliography{[LOCAL_BIB_FILE]}

# % with biblatex you would run something like
jabref -n --aux main.aux,[LOCAL_BIB_FILE] [CENTRAL_BIB_FILE]
## and again switch which bib file you're working with

alanocallaghan

library("ggplot2")
library("ggdist")
library("latex2exp")

set.seed(42)
means <- rnorm(4)
df_slabplot <- rbind(
    data.frame(
        method = "hmc",
        bj = rnorm(4000, mean = rep(means, each = 1000)),