plot.deeptools: Plot deeptools plots.

Description Usage Arguments Value

View source: R/plot.deeptools.R

Description

deeptools –outFileNameMatrix in, plot out

Usage

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## 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 July 23, 2018, 4:13 a.m.