plot.deeptools: Plot deeptools plots.

In robinweide/RHWlib: Simple functions to make life... simpler.

Description

deeptools –outFileNameMatrix in, plot out

Usage

## S3 method for class 'deeptools'
plot(dt, zlim, profileZlim, sampleNames, name = "",
  heatmap = T, smooth = F, smoothPar = 0.1, order = NULL,
  enrichment = F, ignoreSamples = NULL, subsample = NULL,
  profileCols = NULL, getTopX = NULL, getBottomX = NULL,
  profileFunct = "mean", sortWidth = 10, focus = 1, increasing = T,
  verbose = T, brewerPal = "Greys", brewerDir = 1)

Arguments

dt	A datatable from fread(mat)
zlim	zlims c(min,max) for heatmap
profileZlim	zlims c(min,max) for profile
sampleNames	Sample names. Duh.
heatmap	Do you also want a heatmap? Tak
order	The order to plot
ignoreSamples	Remove which samples from output?
subsample	Sample matrix to N rows to test function
profileCols	Vector of colors for profile-plots
getTopX	Prints the top-X values (no plot!)
getBottomX	Prints the bottom-X values (no plot!)
profileFunct	Funciton to make profile-plots (mean, median, sum, absSum)
sortWidth	Percentage of columns to sort on (aligned on center)
focus	Sort on which sample?
increasing	Sort increasing?
verbose	Chatty?

Value

A plot and a df (invisible)

robinweide/RHWlib documentation built on May 7, 2019, 8:03 a.m.