scCustomize (version 3.0.1)

Iterate_Plot_Density_Joint: Iterative Plotting of Gene Lists using Custom Joint Density Plots

Description

Create and save plots for gene list with single command. Requires Nebulosa package from Bioconductor.

Usage

Iterate_Plot_Density_Joint(
  seurat_object,
  gene_list,
  viridis_palette = "magma",
  custom_palette = NULL,
  pt.size = 1,
  file_path = NULL,
  file_name = NULL,
  file_type = NULL,
  single_pdf = FALSE,
  output_width = NULL,
  output_height = NULL,
  dpi = 600,
  reduction = NULL,
  combine = TRUE,
  joint = NULL,
  ...
)

Value

Saved plots

Arguments

seurat_object

Seurat object name.

gene_list

a list of vectors of genes to plot jointly. Each entry in the list will be plotted for the joint density. All entries in list must be greater than 2 features. If a named list is provided then the names for each list entry will be incorporated into plot title if single_pdf = TRUE or into file name if FALSE.

viridis_palette

color scheme to use.

custom_palette

color for non-expressed cells.

pt.size

Adjust point size for plotting.

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). `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.

reduction

Dimensionality Reduction to use (if NULL then defaults to Object default)

combine

Create a single plot? If FALSE, a list with ggplot objects is returned.

joint

NULL. This function only supports joint = FALSE. Leave as NULL to generate plots. To iterate joint plots see function: Iterate_Plot_Density_Joint.

...

Extra parameters passed to plot_density.

Examples

if (FALSE) {
Iterate_Plot_Density_Joint(seurat_object = object, gene_list = DEG_list, viridis_palette = "magma",
file_path = "plots/", file_name = "joint_plots", file_type = ".jpg", dpi = 600)
}