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