Iterate_DimPlot_bySample: Iterate DimPlot By Sample

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Iterate DimPlot By Sample

Description

Iterate DimPlot by orig.ident column from Seurat object metadata

Usage

Iterate_DimPlot_bySample(
  seurat_object,
  sample_column = "orig.ident",
  file_path = NULL,
  file_name = NULL,
  file_type = NULL,
  single_pdf = FALSE,
  output_width = NULL,
  output_height = NULL,
  dpi = 600,
  color = "black",
  no_legend = TRUE,
  title_prefix = NULL,
  reduction = NULL,
  dims = c(1, 2),
  pt.size = NULL,
  raster = NULL,
  ...
)

Arguments

seurat_object	Seurat object name.
sample_column	name of meta.data column containing sample names/ids (default is "orig.ident").
file_path	directory file path and/or file name prefix. Defaults to current wd.
file_name	name suffix to append after sample name.
file_type	File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
single_pdf	saves all plots to single PDF file (default = FALSE). 'file_type“ must be .pdf
output_width	the width (in inches) for output page size. Default is NULL.
output_height	the height (in inches) for output page size. Default is NULL.
dpi	dpi for image saving.
color	color scheme to use.
no_legend	logical, whether or not to include plot legend, default is TRUE.
title_prefix	Value that should be used for plot title prefix if no_legend = TRUE. If NULL the value of meta_data_column will be used. Default is NULL.
reduction	Dimensionality Reduction to use (default is object default).
dims	Dimensions to plot.
pt.size	Adjust point size for plotting.
raster	Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
...	Extra parameters passed to DimPlot.

Value

A ggplot object

Examples

## Not run: 
Iterate_DimPlot_bySample(seurat_object = object, file_path = "plots/", file_name = "tsne",
file_type = ".jpg", dpi = 600, color = "black")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.