interactiveDotplot: Interactive triwise dotplot
In saeyslab/triwise: Gene expression changes in three biological conditions

Description Usage Arguments Value Examples

Draw an interactive triwise dotplot using a html widget

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)

`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

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

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)