plotDotplot: Creating a dotplot

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

Description

Plot a dotplot

Usage

plotDotplot(barycoords, Gdiffexp = rownames(barycoords), Goi = NULL,
  Coi = attr(barycoords, "conditions"), colorby = "diffexp",
  colorvalues = NULL, rmax = 5, showlabels = TRUE,
  sizevalues = stats::setNames(c(0.5, 2), c(FALSE, TRUE)),
  alphavalues = stats::setNames(c(0.8, 0.8), c(FALSE, TRUE)),
  barycoords2 = NULL, baseangle = 0)

Arguments

barycoords	Dataframe containing for every gene its barycentric coordinates, as returned by transformBarycentric
Gdiffexp	Differentially expressed genes
Goi	Genes of interest, a character or numeric vector to plot one set of genes, a named list containing different such vectors to plot multiple gene sets
Coi	Character vector specifying the names of the three biological conditions, used for labelling
colorby	Color by differential expression ("diffexp") or by log fold-change ("z")
colorvalues	Color values, different syntax depending on the colorby parameter: diffexp: Named list with colors. First part of the name denotes whether a gene is differentially expressed ('diffexp' or 'nodiffexp'). The second part denotes the name of the gene set. Genes not within a gene set are denoted by 'all'. For example: list(diffexpall="#000000", nodiffexpall="#AAAAAA", nodiffexpgset="#FFAAAA", diffexpgset="#FF0000") z: A character vector of color values, used to generate the color gradient
rmax	Number denoting the maximal radius of the grid. All points outside of the grid will be clipped on the boundaries.
showlabels	Whether to show labels on the grid
sizevalues	Named list with the size of each dot if differentially expressed (TRUE) or not (FALSE)
alphavalues	Named list with the alpha value of each dot if differentially expressed (TRUE) or not (FALSE)
barycoords2	Dataframe containing for every gene a second set of barycentric coordinates, as returned by transformBarycentric. An arrow will be drawn from the coordinates in 'barycoords' to those in 'barycoords2'
baseangle	The angle by which to rotate the whole plot (default to 0)

Value

A ggplot2 plot, which can be used for further customization

Examples

data(vandelaar)
Eoi <- limma::avearrays(vandelaar, Biobase::phenoData(vandelaar)$celltype)
Eoi = Eoi[,c("YS_MF", "FL_mono", "BM_mono")]
barycoords = transformBarycentric(Eoi)
plotDotplot(barycoords)

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)
Gdiffexp =(1:1000)[barycoords$r > 1]
plotDotplot(barycoords)
plotDotplot(barycoords, Gdiffexp)
plotDotplot(barycoords, Gdiffexp, 1:100)
plotDotplot(barycoords, Gdiffexp, list(a=1:100, b=sample(100:1000, 50)))

Zouter/triwise documentation built on May 10, 2019, 1:59 a.m.