Iterate_Plot_Density_Custom {scCustomize} | R Documentation |
Iterative Plotting of Gene Lists using Custom Density Plots
Description
Create and save plots for gene list with single command. Requires Nebulosa package from Bioconductor.
Usage
Iterate_Plot_Density_Custom(
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,
dpi = 600,
reduction = NULL,
combine = TRUE,
joint = FALSE,
...
)
Arguments
seurat_object |
Seurat object name. |
gene_list |
vector of genes to plot. If a named vector is provided then the names for each gene
will be incorporated into plot title if |
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. |
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 |
... |
Extra parameters passed to |
Value
Saved plots
Examples
## Not run:
Iterate_Plot_Density_Custom(seurat_object = object, gene_list = DEG_list, viridis_palette = "magma",
file_path = "plots/", file_name = "_density_plots", file_type = ".jpg", dpi = 600)
## End(Not run)