Iterative Plotting of Gene Lists using Custom Joint Density Plots — Iterate_Plot_Density

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

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,
  ...
)

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.

Value

Saved plots

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)
}