gsvaSCE: gsvaSCE

Description Usage Arguments Value Functions

View source: R/GSVA.R

Description

Run GSVA analysis on a SCtkExperiment object.

Usage

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

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

Arguments

inSCE

Input SCtkExperiment object. Required

useAssay

Indicate which assay to use. The default is "logcounts"

pathwaySource

The pathway source if "Manual Input", the pathwayNames should be rowData annotations that are (0,1) vectors. If, "MSigDB c2 (Human, Entrez ID only)", the pathwayNames should be pathways from MSigDB c2 or "ALL" to run on all available pathways.

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


singleCellTK documentation built on Dec. 2, 2018, 6 p.m.