grimbough’s gists

grimbough / rhdf5_read_nullable.R

Created April 24, 2023 12:53

Example of reading anndata nullable with rhdf5

	library(rhdf5)
	packageVersion("rhdf5")
	#> [1] '2.43.6'

	h5File <- system.file("testfiles", "nullable_examples.h5", package = "rhdf5")
	h5read(h5File, name = "nullable_boolean")
	#> [1] TRUE FALSE NA
	h5read(h5File, name = "nullable_integer")
	#> [1] 1 NA 3 4

grimbough / post_add_equation_links.R

Created October 19, 2022 09:01

Adding anchor links to equations in Quarto

	## expects to be passed HTML that has already been read with readLines()
	insert_anchor_JS <- function(lines) {

	## we'll look for this JavaScript entry in the html
	pattern <- "const anchorJS = new window.AnchorJS();"

	## this is the new JavaScript to insert
	insert <- " const anchorJS_eq = new window.AnchorJS();
	anchorJS_eq.options = {
	placement: 'left',

grimbough / rstudio-download-logs.R

Created April 13, 2022 13:18

Plotting download counts of various R versions from R Studio CRAN mirror

	library(tidyverse)
	library(lubridate)
	library(scales)

	## generate names for log files
	start <- as.Date('2013-01-01')
	today <- as.Date('2022-04-10')
	all_days <- seq(start, today, by = 'day')
	year <- as.POSIXlt(all_days)$year + 1900

grimbough / h5_combine_vs_select_hslab.c

Created March 5, 2021 14:05

Comparing H5Sselect_hyperslab and H5Scombine_hyperslab

	/*
	* Confirming hyperslab issue remains when combining two selections
	* using H5Scombine_select
	*/

	#include <hdf5.h>
	#include <stdlib.h>

	#define FILE "subset.h5"
	#define DATASETNAME "IntArray"

grimbough / example.Rmd

Created June 3, 2019 14:48

Reusing code chunks from an existing Rmarkdown document

	This code chunk will extract all code blocks from `example.Rmd` and write them to a temporary file, preservining chunk options. It will then read them and make those chunks avaliable in the current R environment when the presentation is knitted.

	```{r include, eval=TRUE, echo=FALSE, include = FALSE}
	tmp_script <- tempfile()
	knitr::purl("example.Rmd", output=tmp_script, quiet = TRUE)
	knitr::read_chunk(tmp_script)
	```

	We can then include a chunk from `example.Rmd` like so:

grimbough / benchmark_index2hyperslab.R

Created January 22, 2019 16:21

Benchmarking improvements in rhdf5 index to hyperslab selection

	BiocManager::install("grimbough/rhdf5", ref = "f06ab6f",
	update = FALSE, ask = TRUE, INSTALL_opts = c('--no-lock'))

	suppressPackageStartupMessages(library(rhdf5))
	suppressPackageStartupMessages(library(microbenchmark))
	suppressPackageStartupMessages(library(ggplot2))
	suppressPackageStartupMessages(library(dplyr))
	suppressPackageStartupMessages(library(stringr))

	h5file <- "/tmpdata/msmith/ExperimentHub/2230"

grimbough / IF015_example.R

Last active November 20, 2018 17:40

Modified example of code provided in https://support.bioconductor.org/p/115224/ to identify error thrown by EBImage


	WD <- tempdir()
	setwd(WD)
	library(EBImage)
	library(tidyverse)

	## download example zip file ad unpack
	download.file('https://www.dropbox.com/s/40e5tfohgdm9wlo/IF015_plate002_test.zip?dl=1',
	destfile = 'IF015_plate002.zip', mode = "wb")
	unzip('IF015_plate002.zip')

grimbough / hyperslab_selection_benchmark.R

Last active November 13, 2018 22:16

Testing performance of H5Sselect_index in the rhdf5 package

	library(rhdf5)

	hslab_bm <- function(m = 10000, n = 10000) {
	## TENxBrainData
	fid <- H5Fopen('/media/Storage/Work/ExperimentHub/1040')
	did <- H5Dopen(h5loc = fid, 'counts')
	sid <- H5Dget_space(did)

	## select first 100 rows and a random (ordered) sample of columns
	index <- list(1:100,

grimbough / hierarchical_layout.R

Created August 3, 2018 20:37

Demonstrating laying out plots in a 'tree' structure using gridExtra

	library(ggplot2)
	library(gridExtra)

	## create 17 plots, where the only element is a number in the centre
	res <- list()
	for(i in 1:17) {
	x <- data.frame(x = 1, y = 1, num = as.character(i))
	res[[i]] <- ggplot(x, aes(x = x, y = y, label = num)) +
	geom_text() +
	theme_void() +

grimbough / BDAvSVD.R

Created February 25, 2018 18:36

Timing BigDataAlgorithms::rsvd against base::svd

	library(TENxBrainData)
	library(ggplot2)
	library(tidyr)

	tenx <- TENxBrainData()

	ncols <- c(1,2,5,10,20,50,100,200,500,1000)

	svd <- bda <- numeric(length = length(ncols))

Mike Smith grimbough