plot_stratum: Display the results of stratify_seurat

In dputhier/dbfmcl: The scigenex package (Single-Cell Informative GENe Explorer)

Display the results of stratify_seurat

Description

Display the results of stratify_seurat

Usage

plot_stratum(
  seurat_obj = NULL,
  gene_name = NULL,
  metadata = NULL,
  intensity_slot = c("data", "counts", "sct"),
  colours_stratum = NULL,
  polar = FALSE
)

Arguments

seurat_obj	A Seurat object.
gene_name	The name of the gene to plot.
metadata	Provide the name of a metadata that will be used instead of genes (i.e. from meta.data) slot of a seurat object.
intensity_slot	The assay slot to use for the gene expression values. Must be one of "sct", "counts", or "data". Default is "sct".
colours_stratum	A set of colors for the stratum.
polar	Whter to use polar coordinates.

Examples

library(Seurat)
library(ggplot2 )
load_example_dataset("7870305/files/lymph_node_tiny_2")
Seurat::SpatialDimPlot(lymph_node_tiny_2)
identity <- Idents(lymph_node_tiny_2)
classes <- ifelse(Idents(lymph_node_tiny_2) == 7, 1, 0)
names(classes) <- names(identity)
h <- display_hull(lymph_node_tiny_2, ident=classes, color="black", delta=1, size_x=3.4, size_y=3)
plot_spatial(lymph_node_tiny_2, metadata = "seurat_clusters", pt_size = 6) + h
strats <- stratify_seurat(lymph_node_tiny_2, ident=classes,
                          colours_stratum = rev(discrete_palette(5, "De1")))
 p <- plot_stratum(strats[[1]], gene_name="CCL19", polar = TRUE, 
                   colours_stratum = rev(discrete_palette(5, "De1")))
p + strats[[3]] + ggplot2::coord_equal()  + Seurat::NoLegend()

dputhier/dbfmcl documentation built on May 31, 2024, 8:57 a.m.