Compute and plot visualizations for marker genes

Compute and plot visualizations for marker genes

plotSeuratGenes(
  inSCE,
  scaledAssayName = "seuratScaledData",
  plotType,
  features,
  groupVariable,
  splitBy = NULL,
  cols = c("lightgrey", "blue"),
  ncol = 1,
  combine = FALSE
)

Arguments

inSCE

Input SingleCellExperiment object.

scaledAssayName

Specify the name of the scaled assay stored in the input object.

plotType

Specify the type of the plot to compute. Options are limited to "ridge", "violin", "feature", "dot" and "heatmap".

features

Specify the features to compute the plot against.

groupVariable

Specify the column name from the colData slot that should be used as grouping variable.

splitBy

Specify the column name from the colData slot that should be used to split samples. Default is NULL.

cols

Specify two colors to form a gradient between. Default is c("lightgrey", "blue").

ncol

Visualizations will be adjusted in "ncol" number of columns. Default is 1.

combine

A logical value that indicates if the plots should be combined together into a single plot if TRUE, else if FALSE returns separate ggplot objects for each feature. Only works when plotType parameter is "feature", "violin" or "ridge". For "heatmap" and "dot", plots for all features are always combined into a single plot. Default FALSE.

Value

Plot object