This function takes a single-column data frame, which is a
single-column subset of the ranked matrix data generated using
rankGenes()
function, and the gene sets of interest as inputs. It plots
the density of ranks for genes in the gene set and overlays a barcode plot
of these ranks. Ranks are normalized by dividing them by the maximum rank.
Densities are estimated using KDE.
plotRankDensity( rankData, upSet, downSet = NULL, isInteractive = FALSE, textSize = 1.5 ) # S4 method for ANY,vector,missing plotRankDensity( rankData, upSet, downSet = NULL, isInteractive = FALSE, textSize = 1.5 ) # S4 method for ANY,GeneSet,missing plotRankDensity( rankData, upSet, downSet = NULL, isInteractive = FALSE, textSize = 1.5 ) # S4 method for ANY,vector,vector plotRankDensity( rankData, upSet, downSet = NULL, isInteractive = FALSE, textSize = 1.5 ) # S4 method for ANY,GeneSet,GeneSet plotRankDensity( rankData, upSet, downSet = NULL, isInteractive = FALSE, textSize = 1.5 )
rankData | one column of the ranked gene expression matrix obtained from
the |
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upSet | GeneSet object or a vector of gene Ids, up-regulated gene set |
downSet | GeneSet object or a vector of gene Ids, down-regulated gene set |
isInteractive | Boolean, determine whether the returned plot is interactive |
textSize | numberic, set the size of text on the plot |
A ggplot object (or a plotly object) with a rank density plot overlayed with a barcode plot
#> Warning: Ignoring unknown aesthetics: text