PctCellsAboveX: Percentage of Cells Above Threshold

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Percentage of Cells Above Threshold

Description

This function calculates the percentage of cells above a specified threshold for a given feature in a Seurat object. It can subset the data based on a specified identity and values.

Usage

PctCellsAboveX(
  obj = combined.obj,
  feature = "TOP2A",
  ident = GetNamedClusteringRuns(obj = obj, v = FALSE)[1],
  threshold = 2,
  suffix = ppp(substitute_deparse(obj), ncol(obj), "thr", threshold),
  box = FALSE,
  ident.box = NULL,
  subset_ident = NULL,
  subset_values = NULL,
  omit.na = TRUE,
  assay = "RNA",
  plot = TRUE,
  caption = NULL,
  ylab = "% cells above threshold",
  ...
)

Arguments

obj	A Seurat object. Default: combined.obj.
feature	The feature to evaluate.
ident	The identity class to split the data by. Default: GetNamedClusteringRuns(obj)1.
threshold	The threshold value to evaluate the feature against. Default: 2.
box	Logical value indicating whether to plot the boxplot. Default: TRUE.
subset_ident	The identity class to subset the data by. Default: NULL.
subset_values	The values of the identity class to keep in the subset. Default: NULL.
omit.na	Logical value indicating whether to omit NA values. Default: TRUE.
assay	The assay to use for feature extraction. Default: 'RNA'.
plot	Logical value indicating whether to plot the results. Default: TRUE.
ylab	The label for the y-axis of the plot. Default: "% cells above threshold".
...	Additional parameters to pass to the plotting function.
box.ident	The identity class to split the data by for individual dots in the boxplot. Ident will be used for the boxes displayed (matching the barplot). Default: NULL.

Value

A named vector with the percentage of cells above the threshold for each identity class.

Examples

## Not run: 
PctCellsAboveX(obj = seurat_object, feature = "GeneA", ident = "CellType", threshold = 1.5)

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.