plotRankDensity: Plot the densities of ranks for one sample

In DavisLaboratory/singscore: Rank-based single-sample gene set scoring method

Plot the densities of ranks for one sample

Description

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.

Usage

plotRankDensity(
  rankData,
  upSet,
  downSet = NULL,
  isInteractive = FALSE,
  textSize = 1.5
)

## S4 method for signature 'ANY,vector,missing'
plotRankDensity(
  rankData,
  upSet,
  downSet = NULL,
  isInteractive = FALSE,
  textSize = 1.5
)

## S4 method for signature 'ANY,GeneSet,missing'
plotRankDensity(
  rankData,
  upSet,
  downSet = NULL,
  isInteractive = FALSE,
  textSize = 1.5
)

## S4 method for signature 'ANY,vector,vector'
plotRankDensity(
  rankData,
  upSet,
  downSet = NULL,
  isInteractive = FALSE,
  textSize = 1.5
)

## S4 method for signature 'ANY,GeneSet,GeneSet'
plotRankDensity(
  rankData,
  upSet,
  downSet = NULL,
  isInteractive = FALSE,
  textSize = 1.5
)

Arguments

rankData	one column of the ranked gene expression matrix obtained from the rankGenes() function, use drop = FALSE when subsetting the ranked gene expression matrix, see examples.
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

Value

A ggplot object (or a plotly object) with a rank density plot overlayed with a barcode plot

Examples

ranked <- rankGenes(toy_expr_se)
plotRankDensity(ranked[,2,drop = FALSE], upSet = toy_gs_up)

DavisLaboratory/singscore documentation built on Nov. 21, 2024, 8:17 a.m.