Iterate_FeaturePlot_scCustom: Iterative Plotting of Gene Lists using Custom FeaturePlots

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

Iterative Plotting of Gene Lists using Custom FeaturePlots

Description

Create and Save plots for Gene list with Single Command

Usage

Iterate_FeaturePlot_scCustom(
  seurat_object,
  features,
  colors_use = viridis_plasma_dark_high,
  na_color = "lightgray",
  na_cutoff = 1e-09,
  split.by = NULL,
  order = TRUE,
  return_plots = FALSE,
  file_path = NULL,
  file_name = NULL,
  file_type = NULL,
  single_pdf = FALSE,
  output_width = NULL,
  output_height = NULL,
  features_per_page = 1,
  num_columns = NULL,
  landscape = TRUE,
  dpi = 600,
  pt.size = NULL,
  reduction = NULL,
  raster = NULL,
  alpha_exp = NULL,
  alpha_na_exp = NULL,
  ...
)

Arguments

seurat_object	Seurat object name.
features	vector of features to plot. If a named vector is provided then the names for each gene will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.
colors_use	color scheme to use.
na_color	color for non-expressed cells.
na_cutoff	Value to use as minimum expression cutoff. To set no cutoff set to NA.
split.by	Variable in ⁠@meta.data⁠ to split the plot by.
order	whether to move positive cells to the top (default = TRUE).
return_plots	logical. Whether to return plots to list instead of saving them to file(s). Default is FALSE.
file_path	directory file path and/or file name prefix. Defaults to current wd.
file_name	name suffix and file extension.
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).
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.
features_per_page	numeric, number of features to plot on single page if single_pdf = TRUE. Default is 1.
num_columns	Number of columns in plot layout (only applicable if single_pdf = TRUE AND features_per_page > 1).
landscape	logical, when plotting multiple features per page in single PDF whether to use landscape or portrait page dimensions (default is TRUE).
dpi	dpi for image saving.
pt.size	Adjust point size for plotting.
reduction	Dimensionality Reduction to use (if NULL then defaults to Object default).
raster	Convert points to raster format. Default is NULL which will rasterize by default if greater than 200,000 cells.
alpha_exp	new alpha level to apply to expressing cell color palette (colors_use). Must be value between 0-1.
alpha_na_exp	new alpha level to apply to non-expressing cell color palette (na_color). Must be value between 0-1.
...	Extra parameters passed to FeaturePlot.

Value

Saved plots

Examples

## Not run: 
Iterate_FeaturePlot_scCustom(seurat_object = object, features = DEG_list,
colors_use = viridis_plasma_dark_high, na_color = "lightgray", file_path = "plots/",
file_name = "tsne", file_type = ".jpg", dpi = 600)

## End(Not run)

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