Iterate Meta Highlight Plot — Iterate_Meta_Highlight

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

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 seurat_object@meta.data 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

if (FALSE) {
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)
}