multi_clUMAP.A4: Plot multiple categorical variables in combined UMAPs

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

Plot multiple categorical variables in combined UMAPs

Description

Generates and saves multiple UMAP plots for clustering results, adjusting the layout and plot dimensions. Supports the generation of plots in different formats and customization of the visual appearance.

Usage

multi_clUMAP.A4(
  obj = combined.obj,
  idents = GetClusteringRuns(obj)[1:4],
  foldername = "clUMAPs_multi",
  plot.reduction = "umap",
  intersectionAssay = c("RNA", "integrated")[1],
  layout = c("tall", "wide", FALSE)[2],
  nr.Col = 2,
  nr.Row = 4,
  cex = round(0.1/(nr.Col * nr.Row), digits = 2),
  label = FALSE,
  legend = !label,
  subdir = TRUE,
  prefix = NULL,
  suffix = NULL,
  background_col = "white",
  aspect.ratio = c(FALSE, 0.6)[2],
  saveGeneList = FALSE,
  w = 8.27,
  h = 11.69,
  scaling = 1,
  format = c("jpg", "pdf", "png")[1],
  ...
)

Arguments

obj	The Seurat object containing clustering information. Default: combined.obj.
idents	A vector of cluster identities to plot. Default: GetClusteringRuns()[1:4].
foldername	The name of the folder to save plots. Default: substitute(ident).
plot.reduction	The dimensionality reduction technique to use for plotting. Default: "umap".
intersectionAssay	The assay to use for intersection. Default: "RNA".
layout	The layout orientation, either "tall", "wide", or FALSE to disable. Default: "wide".
nr.Col	Number of columns in the plot grid. Default: 2.
nr.Row	Number of rows in the plot grid. Default: 4.
cex	The character expansion size for plot text, automatically adjusted. Default: round(0.1 / (nr.Col * nr.Row), digits = 2).
label	Logical indicating if labels should be displayed on the plots. Default: FALSE.
legend	Logical indicating if a legend should be included in the plots. Default: !label.
subdir	Logical indicating if a subdirectory should be created for saving plots. Default: TRUE.
prefix	Optional prefix for plot filenames. Default: NULL.
suffix	Optional suffix for plot filenames. Default: NULL.
background_col	The background color of the plot. Default: "white".
aspect.ratio	The aspect ratio of the plot, FALSE to disable fixed ratio. Default: 0.6.
saveGeneList	Logical indicating if a list of genes should be saved. Default: FALSE.
w	The width of the plot in inches. Default: 8.27.
h	The height of the plot in inches. Default: 11.69.
scaling	The scaling factor to apply to plot dimensions. Default: 1.
format	The file format for saving plots. Default: "jpg".
...	Additional arguments passed to plotting functions.

Value

Invisible NULL. Plots are saved to files.

Examples

## Not run: 
multi_clUMAP.A4(idents = c("S1", "S2"), obj = YourSeuratObject)

## End(Not run)

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