grimbough

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

## 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

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

/*
 *  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

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

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

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

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

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

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))