interactiveDotplot: Interactive triwise dotplot

Description Usage Arguments Value Examples

Description

Draw an interactive triwise dotplot using a html widget

Usage

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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

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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)

saeyslab/triwise documentation built on May 29, 2019, 12:56 p.m.