README.md

In drmjc/mjcgraphics: mjc's graphics library

mjcgraphics

An R package of various graphics plots and wrappers. Mostly using base graphics for bioinformatics and microarray data.

INSTALLATION

# install Bioconductor if you haven't already done so:
source("http://bioconductor.org/biocLite.R")
biocLite()

# install required CRAN/Bioconductor packages
library(BiocInstaller)
biocLite(c("limma", "lumi"))
install.packages(c("gplots", "gtools", "RColorBrewer", "devtools"))

library(devtools)
install_github("drmjc/excelIO")
install_github("drmjc/mjcbase")
install_github("drmjc/mjcgraphics")

Popular Functions

1) Convenient wrappers around png(), jpeg(), pdf() to create standard sized images

?plotting.devices
?png.VGA, ?pdf.A4, etc...

2) Correspondence-at-the-top (CAT) plots

?catplot
?catplot.vs.random

3) plot all rows (as lines) or columns (as density plots) of a matrix

?plot.matrix
?plot.density.matrix

4) convenient grids

?hgrid, ?vgrid, ?grid.percentiles

5) Combination of a sorted scatter plot, and boxplot

?comboplot_scatter_boxplot

6) Errorbar plots, and staistical significance

?errorbarplot, ?pvalue.stars

drmjc/mjcgraphics documentation built on May 15, 2019, 2:40 p.m.