plotRoseplot: Plot the directional distribution of genes

Description Usage Arguments Value Examples

View source: R/visualize.R

Description

A rose plot shows the distribution of a given set of genes in different directions.

Usage

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plotRoseplot(barycoords, Gdiffexp = rownames(barycoords),
  Goi = rownames(barycoords), size = "surface", relative = TRUE,
  showlabels = TRUE, Coi = attr(barycoords, "conditions"), nbins = 12,
  bincolors = grDevices::rainbow(nbins, start = 0, v = 0.8, s = 0.6),
  rmax = "auto", baseangle = 0)

Arguments

barycoords

Dataframe containing barycentric coordinates as returned by transformBarycentric.

Gdiffexp

List of differentially expressed genes

Goi

List of genes of interest

size

Should the 'radius' or the 'surface' of a circle sector denote the number of genes differentially expressed in a particular direction

relative

Whether to show the relative number of genes or the absolute number of genes

showlabels

Whether to label the grid

Coi

Names of the three biological conditions, used for labelling

nbins

Number of bins, should be a multiple of 3 to make sense

bincolors

Colors of every bin, defaults to a rainbow palette

rmax

Number or "auto" (default), denotes the maximal radius of the grid.

baseangle

The angle by which to rotate the whole plot (default to 0)

Value

A ggplot2 plot, which can be used to further customize the plot

Examples

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Eoi = matrix(rnorm(1000*3, sd=0.5), 1000, 3, dimnames=list(1:1000, c(1,2,3)))
Eoi[1:100,1] = Eoi[1:100,1] + 1
barycoords = transformBarycentric(Eoi)
plotRoseplot(barycoords)
plotRoseplot(barycoords, (1:1000)[barycoords$r > 1])
plotRoseplot(barycoords, (1:1000)[barycoords$r > 1], 1:100)

Zouter/triwise documentation built on June 3, 2017, 10:50 a.m.