Iterate DimPlot By Sample — Iterate_DimPlot

Iterate DimPlot by orig.ident column from Seurat object metadata

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

if (FALSE) {
Iterate_DimPlot_bySample(seurat_object = object, file_path = "plots/", file_name = "tsne",
file_type = ".jpg", dpi = 600, color = "black")
}