plot_spatial: XY scatter plot of Visium data with hexagonal spots.

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

XY scatter plot of Visium data with hexagonal spots.

Description

Given a Seurat Spatial object, this function creates a scatter plot of the spatial expression of a gene across spots, where the X and Y coordinates represent the spatial location of spots and the color represents the expression level of the gene. This function as been tested with visium data at the moment. Defaut shape is hexagon.

Usage

plot_spatial(
  seurat_obj = NULL,
  gene_name = NULL,
  metadata = NULL,
  intensity_slot = c("data", "counts", "sct"),
  title = "",
  size_title = 10,
  face_title = c("plain", "italic", "bold", "bold.italic"),
  legend = TRUE,
  barwidth = 1,
  barheight = 3,
  axis = TRUE,
  pt_size = 3.6,
  pt_shape = 6,
  pt_star = TRUE,
  stroke = 0,
  colours = colors_for_gradient("Ju1"),
  coord_flip = T
)

Arguments

seurat_obj	A Seurat object containing spatial expression data.
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".
title	The title of the plot. Default is an empty string.
size_title	The size of the title.
face_title	Font face for the title. Possible values are “plain”, “italic”, “bold” and “bold.italic”.
legend	Whether to display a legend for the color scale. Default is FALSE.
barwidth	A numeric or a grid::unit() object specifying the width of the colourbar. Default value is legend.key.width or legend.key.size in theme() or theme.
barheight	A numeric or a grid::unit() object specifying the height of the colourbar. Default value is legend.key.height or legend.key.size in theme() or theme.
axis	Whether to display a axis for the color scale. Default is FALSE.
pt_size	The size of the points in the plot. Default is 2.1.
pt_shape	The shape of the points in the plot. Default is 16 (a circle).
pt_star	A boolean. Whether to use ggstar shapes.
stroke	The thickness of margin of points.
colours	A vector of colors.
coord_flip	Whether to flip coordinates.

Value

A ggplot2 object containing the scatter plot.

Examples

library(Seurat)
load_example_dataset("7870305/files/lymph_node_tiny_2")
plot_spatial(seurat_obj = lymph_node_tiny_2, gene_name = "CCL22", intensity_slot="data", pt_size=6)
plot_spatial(seurat_obj = lymph_node_tiny_2, metadata = "nCount_Spatial", pt_size=6)
hull <- display_hull(lymph_node_tiny_2, 
        ident=ifelse(Seurat::Idents(lymph_node_tiny_2) %in% 7, 1, 0),
        delta=1, size_x=3.4, size_y=3, color="black")
p <- plot_spatial(seurat_obj = lymph_node_tiny_2, gene_name = "VPREB3", intensity_slot="data", pt_size=6)
p + hull

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