Iterative Plotting of Gene Lists using Custom FeaturePlots — Iterate_FeaturePlot

Create and Save plots for Gene list with Single Command

Iterate_FeaturePlot_scCustom(
  seurat_object,
  features,
  gene_list = deprecated(),
  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,
  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.
gene_list: soft-deprecated. See features.
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).
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

if (FALSE) {
Iterate_FeaturePlot_scCustom(seurat_object = object, gene_list = DEG_list,
colors_use = viridis_plasma_dark_high, na_color = "lightgray", file_path = "plots/",
file_name = "tsne", file_type = ".jpg", dpi = 600)
}