plotCombinedMatrix {rnaCrosslinkOO}

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

Description

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

Usage

plotCombinedMatrix(
  cds,
  type1 = "original",
  type2 = "original",
  sample1 = 1,
  sample2 = 1,
  directory = 0,
  a = 1,
  b = 50,
  c = 1,
  d = 50,
  h = 3,
  returnData = FALSE
)

Arguments

cds

A rnaCrosslinkDataSet object

type1

The analysis stage to plot on the upper half of the heatmap

type2

The analysis stage to plot on the lower half of the heatmap

sample1

The sample number to plot on the upper half of the heatmap

sample2

The sample number to plot on the upper half of the heatmap

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)

returnData

if TRUE matrix is returned instead of plotting

Value

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

Examples

cds = makeExamplernaCrosslinkDataSet()

plotCombinedMatrix(cds,
            type1 = "original",
            type2 = "noHost",
            b = rnaSize(cds),
            d = rnaSize(cds))