StressUMAP: Wrapper for clUMAP with Thresholding and Plotting

In jn-goe/gruffi: Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.

Wrapper for clUMAP with Thresholding and Plotting

Description

This function applies thresholding to granule scores within a specified object and column, inverts the thresholding if a specific miscellaneous name is provided, and then calls clUMAP for plotting based on the thresholded values.

Plot Stress Assignment UMAP after running the gruffi pipeline

Usage

StressUMAP(
  obj = combined.obj,
  colname = "is.Stressed",
  GO.terms = names(obj@misc$gruffi$GO),
  title = paste("Stress identification"),
  suffix = NULL,
  ...
)

StressUMAP(
  obj = combined.obj,
  colname = "is.Stressed",
  GO.terms = names(obj@misc$gruffi$GO),
  title = paste("Stress identification"),
  suffix = NULL,
  ...
)

Arguments

obj	An object containing the data and miscellaneous threshold information. Default is combined.obj.
colname	Name of the column containing granule scores. Default is 'RNA_snn_res.6.reassigned_cl.av_GO:0042063'.
GO.terms	used for the computation
title	Title of the plot. Default: "Stress identification".
suffix	Suffix to append to the plot/file name. Default: NULL.
...	Additional arguments to be passed to clUMAP.
miscname	Name of the miscellaneous threshold information within obj@misc$gruffi. Default is 'thresh.stress.ident1'.
auto	Automatically flip filtering

Examples

# Assuming combined.obj is available and properly formatted
customClUMAPWrapper(
  combined.obj,
  "RNA_snn_res.6.reassigned_cl.av_GO:0042063",
  "thresh.stress.ident1"
)

StressUMAP(combined.obj)

jn-goe/gruffi documentation built on Nov. 7, 2024, 10:38 p.m.