DotPlotwithModuleScore: DotPlotwithModuleScore

In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

DotPlotwithModuleScore

Description

Adapted from Seurat::DotPlot but adds the module score per group.

Usage

DotPlotwithModuleScore(
  object,
  assay = NULL,
  features,
  featureDat = featureDat,
  cols = c("lightgrey", "blue"),
  col.min = -2.5,
  col.max = 2.5,
  dot.min = 0,
  dot.scale = 6,
  idents = NULL,
  group.by = NULL,
  split.by = NULL,
  cluster.idents = FALSE,
  clusters = "sampleNames",
  scale = TRUE,
  scale.by = "radius",
  scale.min = NA,
  scale.max = NA
)

Arguments

object	A Seurat object.
assay	The assay to be used for plotting. Defaults to NULL, in which case the default assay of the object is used.
features	A list of character vectors of gene names in "symbol" annotation (SCHNAPPs specific).
featureDat	A data frame containing information about features, particularly the "symbol" column.
cols	A vector of colors for plotting.
col.min	Minimum value for color scaling.
col.max	Maximum value for color scaling.
dot.min	Minimum value for dot scaling.
dot.scale	Scaling factor for dot size.
idents	Identifiers for cells.
group.by	Grouping variable.
split.by	Variable to split the plot by.
cluster.idents	Boolean indicating whether to cluster identifiers.
clusters	Column name for grouping identifiers.
scale	Logical indicating whether to scale the data.
scale.by	The type of scaling to be applied ('size' or 'radius').
scale.min	Minimum value for scaling.
scale.max	Maximum value for scaling.

Value

A ggplot2 object representing the DotPlot with module scores.

C3BI-pasteur-fr/UTechSCB-SCHNAPPs documentation built on Sept. 8, 2024, 12:44 a.m.