multiFeaturePlot.A4: multiFeaturePlot.A4

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

multiFeaturePlot.A4

Description

Save multiple FeaturePlots, as jpeg, on A4 for each gene, which are stored as a list of gene names.

Usage

multiFeaturePlot.A4(
  list.of.genes,
  obj = combined.obj,
  subdir = TRUE,
  foldername = substitute(list.of.genes),
  subtitle.from.names = TRUE,
  plot.reduction = "umap",
  intersectionAssay = c("RNA", "integrated")[1],
  layout = c("tall", "wide", FALSE)[2],
  colors = c("grey", "red"),
  nr.Col = 2,
  nr.Row = 4,
  raster = if (ncol(obj) > 1e+05) TRUE else FALSE,
  cex = round(0.1/(nr.Col * nr.Row), digits = 2),
  cex.min = if (raster) TRUE else FALSE,
  gene.min.exp = "q01",
  gene.max.exp = "q99",
  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

list.of.genes	List of gene names for which the plots are to be generated. No default.
obj	Seurat object, Default: combined.obj
subdir	Should plots be saved in a sub-directory? Default: TRUE.
foldername	Folder name to save the generated plots. Default: The name of the list of genes.
subtitle.from.names	Should the subtitle be extracted from the names of the gene symbols, eg: c("Astrocytes" = "AQP4") ? Default: TRUE.
plot.reduction	Dimension reduction technique to use for plots. Default: 'umap'
intersectionAssay	The assay to intersect with, either 'RNA' or 'integrated'. Default: 'RNA'
layout	Layout orientation of the plot. Default: 'wide'
colors	Vector of colors to be used in the plot. Default: c("grey", "red")
nr.Col	Number of columns in the plot grid. Default: 2
nr.Row	Number of rows in the plot grid. Default: 4
cex	Point size in the plot. Default: round(0.1/(nr.Col * nr.Row), digits = 2)
gene.min.exp	Minimum gene expression level for plotting. Default: 'q01'
gene.max.exp	Maximum gene expression level for plotting. Default: 'q99'
prefix	Prefix for the plot filenames. Default: NULL
suffix	Suffix for the plot filenames. Default: NULL
background_col	Background color of the plots. Default: "white"
aspect.ratio	Should the aspect ratio be fixed? Default: Yes, at 0.6
saveGeneList	Should the list of genes be saved? Default: FALSE.
w	Width of the plot. Default: 8.27
h	Height of the plot. Default: 11.69
scaling	Scaling factor for plot size. Default: 1
format	Format to save the plot file. Default: 'jpg'
...	Pass any other parameter to the internally called functions (most of them should work).

See Also

tic plot_grid

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