interactiveDotplot: Interactive triwise dotplot

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

Description

Draw an interactive triwise dotplot using a html widget

Usage

interactiveDotplot(Eoi, Gdiffexp = rownames(Eoi), Goi = c(),
  Glabels = rownames(Eoi), Gpin = c(), Coi = colnames(Eoi),
  colorvalues = NULL, rmax = 5, sizevalues = c(`TRUE` = 2, `FALSE` = 0.5),
  alphavalues = c(`TRUE` = 0.8, `FALSE` = 0.8), plotLocalEnrichment = FALSE,
  width = NULL, height = NULL)

Arguments

Eoi	Expression matrix with the three conditions in the columns
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
Glabels	Labels for every gene if different from the rownames of 'Eoi'
Gpin	Pinned genes, if 'NULL' will automatically choose the top 20 most differentially expressed genes
Coi	Character vector specifying the names of the three biological conditions, used for labelling
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.
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)
plotLocalEnrichment	Whether to plot local enrichment as a ring around the dotplot
width	Width of the plot
height	Height of the plot

Value

A htmlwidget object, which can be exported to an svg using saveWidget

Examples

data(vandelaar)
Eoi <- limma::avearrays(vandelaar, Biobase::phenoData(vandelaar)$celltype)
Eoi = Eoi[,c("YS_MF", "FL_mono", "BM_mono")]
barycoords = transformBarycentric(Eoi)
## Not run: 
interactiveDotplot(barycoords)

## End(Not run)

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]

## Not run: 
interactiveDotplot(Eoi)
interactiveDotplot(Eoi, Gdiffexp)
interactiveDotplot(Eoi, as.character(Gdiffexp), as.character(1:10), as.character(1:1000))
interactiveDotplot(Eoi, as.character(Gdiffexp), as.character(1:10), as.character(1:1000),
   c(50, 200))

## End(Not run)

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