gsvaSCE {singleCellTK} | R Documentation

## Run GSVA analysis on a SingleCellExperiment object

### 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

[Package singleCellTK version 2.2.0 Index]