Helper function for QC plots by generating intensity count data

Usage

statPlot(
  seurat.obj,
  group.by = NULL,
  assay = "Spatial",
  slot = "counts",
  bottom.cutoff = NULL,
  top.cutoff = NULL,
  log.data = FALSE,
  verbose = FALSE
)

Arguments

seurat.obj: Seruat object containing the intensity data.
group.by: Character string specifying the meta.data column to group by (default = NULL).
assay: Character string defining the name of the Seurat Object assay to pull the corresponding intensity data from (default = "Spatial").
slot: Character string defining the name of the slot within the Seurat Object assay to pull the corresponding intensity data from (default = "counts").
bottom.cutoff: Numeric value defining the percent of data to exclude for the lower end of the distribution. A bottom.cutoff = 0.05 will remove the bottom 5% of data point (default = NULL).
top.cutoff: Numeric value defining the percent of data to exclude for the upper end of the distribution. A top.cutoff = 0.05 will remove the top 5% of data point (default = NULL).
log.data: Boolean value indicating whether to log transform the y-axis values (default = FALSE).
verbose: Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = FALSE).

Value

A data.frame containing the relative transformed and sum counts required for various QC plots

Examples

# df <- statPlot(SeuratObj, group.by = "sample", bottom.cutoff = 0.05, top.cutoff = 0.05, log.data = TRUE)