wolfganghuber

library("EBImage")
im = readImage("Senza nome.png")
r = im[,,1]
g = im[,,2]
b = im[,,3]
brg = r+g+b
hist(brg, breaks = 100)
display(brg)
white = brg > 1.5
r[white] = 1

wolfganghuber

# Code is based on Pete Hickey's and Lori Kern's post in https://support.bioconductor.org/p/109502/
  
library("rvest")
library("ggplot2")
library("magrittr")
library("dplyr")

bioc_pkgs = read_html("http://bioconductor.org/about/release-announcements")
bioc_pkgs_tbl = html_nodes(bioc_pkgs, "table")[[1]] |> html_table()

wolfganghuber

# BiocManager is available from CRAN and is convenient for installing Bioconductor packages such as EBImage
if (!("EBImage" %in% installed.packages()))
  BiocManager::install("EBImage")

library("EBImage")

x = readImage("https://pbs.twimg.com/media/EmPRWjyVoAEBIBI?format=jpg&name=4096x4096", type = "jpeg")

# explore the image
display(x)

wolfganghuber

indir  = "..."
outdir = "..."
passwd = "BLA"
files = dir(path, pattern = "??-*pw.pdf")

for (f in files) {
  args = sprintf("-q -dNOPAUSE -dBATCH -sDEVICE=pdfwrite -sPDFPassword=%s -sOutputFile=%s -c .setpdfwrite -f %s", 
                passwd,
                file.path(outdir, sub("_pw.pdf$", ".pdf", f)), 
                file.path(indir, f))

wolfganghuber

---
title: "Speeding up 'loopy' R code"
author: "Wolfgang Huber"
output: BiocStyle::html_document
---

```{r global_options, include = FALSE}
```

# Versions of this document

wolfganghuber

wolfganghuber

---
title: "Code for Fig.2 in DESeq2 paper, with DESeq2 >= 1.16"
author:
- name: Wolfgang Huber
output:
  BiocStyle::html_document2
vignette: |
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}