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,
dpi = 600,
raster = NULL,
...
)Seurat object name.
Name of the column in seurat_object@meta.data slot to pull value from for highlighting.
The order in which to plot each level within meta_data_column if single_PDF is TRUE.
logical. Whether or not to sort and relevel the levels in meta_data_column if
single_PDF is TRUE. Default is TRUE.
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.
non-highlighted cell colors.
point size for both highlighted cluster and background.
logical, whether or not to remove plot legend and move to plot title. Default is FALSE.
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.
Dimensionality Reduction to use (if NULL then defaults to Object default).
directory file path and/or file name prefix. Defaults to current wd.
name suffix to append after sample name.
File type to save output as. Must be one of following: ".pdf", ".png", ".tiff", ".jpeg", or ".svg".
saves all plots to single PDF file (default = FALSE). `file_type`` must be .pdf
dpi for image saving.
Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
Extra parameters passed toDimPlot.
Saved plots
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)
}