plotRoseplot: Plot the directional distribution of genes

In Zouter/triwise: Gene expression changes in three biological conditions

Description

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

Usage

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

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 May 10, 2019, 1:59 a.m.