bb_gene_dotplot: Make a dotplot of gene expression by cell population

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

Make a dotplot of gene expression by cell population

Description

Make a dotplot of gene expression by cell population

Usage

bb_gene_dotplot(
  cds,
  markers,
  group_cells_by,
  reduction_method = "UMAP",
  norm_method = c("size_log", "log_only"),
  scale_expression_by_gene = FALSE,
  lower_threshold = 0,
  max.size = 10,
  group_ordering = "bicluster",
  gene_ordering = NULL,
  pseudocount = 1,
  scale_max = 3,
  scale_min = -3,
  colorscale_name = NULL,
  sizescale_name = NULL,
  ...
)

Arguments

cds	A cell data set object
markers	A character vector of genes to plot
group_cells_by	A cds colData column. Use "multifactorial" to pick 2 categorical variables to put on X axis and to facet by. See ordering below.
norm_method	How to normalize gene expression. Size_factor and log normalized or only log normalized.
scale_expression_by_gene	Whether to scale expression values according to gene. Defaults to FALSE.
lower_threshold	Lower cutoff for gene expression
max.size	The maximum size of the dotplot
group_ordering	Defaults to "biclustering" method from pheatmap. Optionally will take a vector of group values to set the axis order explicitly. If using group_cells_by = "multifactorial" you will need a df to define facet and axis levels. See example.
gene_ordering	Optional vector of gene names to order the plot.
pseudocount	Add to zero expressors. Default = 1
scale_max	Expression scale max
scale_min	Expression scale min
colorscale_name	Label for the color scale
sizescale_name	Label for the size scale
...	Additional parameters to pass to facet_wrap.

Value

A ggplot

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.