plotCombinedMatrix: Plots a contact map of two chosen samples for chosen stages...

In JLP-BioInf/comradesOO: Analysis of RNA Crosslinking Data

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))

JLP-BioInf/comradesOO documentation built on April 28, 2024, 4:22 a.m.