plotDispersion: Plot the score v.s. despersion for all samples

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

Description

This function takes the output from the simpleScore() function and generates scatter plots of score vs. dispersion for the total score, the up score and the down score of samples. If you wish to use the plotting function but with some customized inputs (instead of outputs from simpleScore function), you need to make sure the formats are the same. To be specific, you need to have columns names "TotalScore" "TotalDispersion" "UpScore" "UpDispersion" "DownScore" "DownDispersion" and rows names as samples.

Usage

plotDispersion(
  scoredf,
  annot = NULL,
  annot_name = "",
  sampleLabels = NULL,
  alpha = 1,
  size = 1,
  textSize = 1.2,
  isInteractive = FALSE
)

Arguments

scoredf	data.frame, generated using the simpleScore() function
annot	any numeric, character or factor annotation provided by the user that needs to be plot. Alternatively, this can be a character specifying the column of scoredf holding the annotation. Annotations must be ordered in the same way as the scores
annot_name	character, legend title for the annotation
sampleLabels	vector of character, sample names to display, ordered in the same way as samples are ordered in the 'scoredf' data.frame and with labels for all samples. Samples whose labels should not be displayed should be left as empty strings or NAs. Default as NULL which means the projected points are not labelled.
alpha	numeric, set the transparency of points
size	numeric, set the size of each point
textSize	numeric, relative text sizes for title, labels, and axis values
isInteractive	Boolean, determine whether the plot is interactive

Value

A ggplot object

Examples

ranked <- rankGenes(toy_expr_se)
scoredf <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn)
plotDispersion(scoredf)
plotDispersion(scoredf, isInteractive = TRUE)

singscore documentation built on Nov. 8, 2020, 8:27 p.m.