gsvaSCE: Run GSVA analysis on a SingleCellExperiment object

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

Run GSVA analysis on a SingleCellExperiment object

Usage

gsvaSCE(inSCE, useAssay = "logcounts", pathwayNames, ...)

gsvaPlot(
  inSCE,
  gsvaData,
  plotType,
  condition = NULL,
  show_column_names = TRUE,
  show_row_names = TRUE,
  text_size = 12
)

Arguments

inSCE	Input SingleCellExperiment object.
useAssay	Indicate which assay to use. The default is "logcounts"
pathwayNames	List of pathway names to run, depending on pathwaySource parameter.
...	Parameters to pass to gsva()
gsvaData	GSVA data to plot. Required.
plotType	The type of plot to use, "Violin" or "Heatmap". Required.
condition	The condition(s) to use for the Violin plot, or the condition(s) to add as color bars above the Heatmap. Required for Violin, optional for Heatmap.
show_column_names	Display the column labels on the heatmap. The default is TRUE
show_row_names	Display the row labels on the heatmap. The default is TRUE.
text_size	Text size for plots. The default is 12

Value

gsvaSCE(): A data.frame of pathway activity scores from GSVA.

gsvaPlot(): The requested plot of the GSVA results.

Functions

• gsvaPlot: Plot GSVA results.

  Plot GSVA Results

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.