bb_gene_dotplot: Make a dotplot of gene expression by cell population
In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

bb_gene_dotplot

R Documentation

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.