Iterate_Meta_Highlight_Plot: Iterate Meta Highlight Plot

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

Iterate Meta Highlight Plot

Description

Iterate the create plots with meta data variable of interest highlighted.

Usage

Iterate_Meta_Highlight_Plot(
  seurat_object,
  meta_data_column,
  new_meta_order = NULL,
  meta_data_sort = TRUE,
  highlight_color = "navy",
  background_color = "lightgray",
  pt.size = NULL,
  no_legend = FALSE,
  title_prefix = NULL,
  reduction = NULL,
  file_path = NULL,
  file_name = NULL,
  file_type = NULL,
  single_pdf = FALSE,
  output_width = NULL,
  output_height = NULL,
  dpi = 600,
  raster = NULL,
  ...
)

Arguments

seurat_object	Seurat object name.
meta_data_column	Name of the column in [e-mail] slot to pull value from for highlighting.
new_meta_order	The order in which to plot each level within meta_data_column if single_PDF is TRUE.
meta_data_sort	logical. Whether or not to sort and relevel the levels in meta_data_column if single_PDF is TRUE. Default is TRUE.
highlight_color	Color to highlight cells (default "navy"). Can provide either single color to use for all clusters/plots or a vector of colors equal to the number of clusters to use (in order) for the clusters/plots.
background_color	non-highlighted cell colors.
pt.size	point size for both highlighted cluster and background.
no_legend	logical, whether or not to remove plot legend and move to plot title. Default is FALSE.
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 (if NULL then defaults to Object default).
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.
raster	Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
...	Extra parameters passed toDimPlot.

Value

Saved plots

Examples

## Not run: 
Iterate_Meta_Highlight_Plot(seurat_object = object, meta_data_column = "sample_id",
highlight_color = "navy", background_color = "lightgray", file_path = "path/",
file_name = "name", file_type = "pdf", single_pdf = TRUE)

## End(Not run)

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