plotMatricesAverage {rnaCrosslinkOO}

plotMatricesAverage

Description

Plots a contact map of all samples for two chosen stages in the analysis, with each chosen stage on separate halves of the contact map

Usage

plotMatricesAverage(
  cds,
  type1 = "original",
  type2 = "blank",
  directory = 0,
  a = 1,
  b = 50,
  c = 1,
  d = 50,
  h = 3
)

Arguments

cds

A rnaCrosslinkDataSet object

type1

The analysis stage to plot on the upper half of the heatmap (use 'blank' to leave this half blank)

type2

The analysis stage to plot on the lower half of the heatmap (use 'blank' to leave this half blank)

directory

An output directory for the heatmap (use 0 for no output)

a

To make a subsetted plot (left value on x)

b

To make a subsetted plot (right value on x)

c

To make a subsetted plot (left value on y)

d

To make a subsetted plot (right value on y)

h

Height of image (inches) ( only useful if plotting)

Value

A heatmap of the reads in the two analysis stages chosen, with each chosen stage on a separate half of the heatmap

Examples

cds = makeExamplernaCrosslinkDataSet()

plotMatricesAverage(cds,
            b = rnaSize(cds),
            d = rnaSize(cds))