qUMAP: Quick UMAP Visualization of Gene Expression and automatically...
In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

View source: R/Seurat.Utils.Visualization.R

qUMAP

R Documentation

Quick UMAP Visualization of Gene Expression and automatically save the plot

Description

Generates a UMAP visualization for a specific feature from a Seurat object, and automatically saves it. Offers options for custom titles, subtitles, saving, and more. Assumes default options for custom titles, subtitles, saving, and more.

Usage

qUMAP(
  feature = "TOP2A",
  obj = combined.obj,
  title = feature,
  sub = NULL,
  reduction = "umap",
  splitby = NULL,
  prefix = NULL,
  suffix = make.names(sub),
  save.plot = MarkdownHelpers::TRUE.unless("b.save.wplots", v = FALSE),
  PNG = TRUE,
  h = 7,
  w = NULL,
  nr.cols = NULL,
  assay = c("RNA", "integrated")[1],
  axes = FALSE,
  aspect.ratio = c(FALSE, 0.6)[1],
  HGNC.lookup = TRUE,
  make.uppercase = FALSE,
  check_for_2D = TRUE,
  qlow = "q10",
  qhigh = "q90",
  caption = .parseBasicObjStats(obj, simple = TRUE),
  ...
)

Arguments

`feature`	Feature to visualize on the UMAP; Default: 'TOP2A'.
`obj`	Seurat object containing single-cell RNA-seq data; Default: `combined.obj`.
`title`	Title of the plot; Default: `feature`.
`sub`	Subtitle of the plot; Default: NULL.
`reduction`	Dimension reduction technique to be used ('umap', 'tsne', or 'pca'); Default: 'umap'.
`splitby`	Column in the metadata to split the cells by; Default: NULL.
`prefix`	Prefix added before the filename; Default: NULL.
`suffix`	Suffix added to the end of the filename; Default: `sub`.
`save.plot`	If TRUE, the plot is saved into a file; Default: `TRUE`.
`PNG`	If TRUE, the file is saved as a .png; Default: `TRUE`.
`h`	Height of the plot in inches; Default: 7.
`w`	Width of the plot in inches; Default: NULL.
`nr.cols`	Number of columns to combine multiple feature plots, ignored if `split.by` is not NULL; Default: NULL.
`assay`	Which assay to use ('RNA' or 'integrated'); Default: 'RNA'.
`axes`	If TRUE, axes are shown on the plot; Default: `FALSE`.
`aspect.ratio`	Ratio of height to width. If TRUE, the ratio is fixed at 0.6; Default: `FALSE`.
`HGNC.lookup`	If TRUE, HGNC gene symbol lookup is performed; Default: `TRUE`.
`make.uppercase`	If TRUE, feature names are converted to uppercase; Default: `FALSE`.
`check_for_2D`	If TRUE, checks if UMAP is 2 dimensional; Default: `TRUE`.
`qlow`	Lower quantile for the color scale; Default: 'q10'.
`qhigh`	Upper quantile for the color scale; Default: 'q90'.
`caption`	Adds a caption to the ggplot object; Default: dynamically generated from `obj`.
`...`	Additional parameters to pass to the internally called functions.

Examples

## Not run: 
if (interactive()) {
  qUMAP(feature = "nFeature_RNA", obj = yourSeuratObject)
  qUMAP(feature = "TOP2A", obj = yourSeuratObject, PNG = FALSE, save.plot = TRUE)
}

## End(Not run)

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