plot_spatial_panel: A planel of XY scatter plots of Visium data with hexagonal...

View source: R/plot_spatial.R

plot_spatial_panelR Documentation

A planel of XY scatter plots of Visium data with hexagonal spots.

Description

This function creates a panel of scatter plots for the spatial expression of a list of genes across spots, where the X and Y coordinates represent the spatial location of spots and the color represents the expression level of the gene.

Usage

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

Arguments

seurat_obj

A Seurat object containing spatial expression data.

genes

A vector of gene names to plot.

metadata

Provide a vector of 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 titles.

face_title

Font face for the title. Possible values are “plain”, “italic”, “bold” and “bold.italic”.

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.

panel_names

A vector of panel names to use for each gene plot.

ncol_layout

Number of columns to use for the panel layout. Default is the ceiling of the number of genes divided by 2.

legend

Whether to display a legend for the color scale. Default is FALSE.

guides

A string specifying how guides should be treated in the layout. See patchwork::plot_layout().

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.

coord_flip

Whether to flip coordinates.

colours

A vector of colors.

Value

A ggplot2 object containing the panel of scatter plots.

Examples

library(Seurat)
load_example_dataset("7870305/files/lymph_node_tiny_2")
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
lymph_node_tiny_2 <- Seurat::AddModuleScore(lymph_node_tiny_2, features = lymph_node_tiny_clusters_2@gene_clusters, nbin = 15)
for(i in 1:nclust(lymph_node_tiny_clusters_2)){ # Normalizing module scores
    tmp <- lymph_node_tiny_2[[paste0("Cluster", i, sep="")]] 
    max_tmp <- max(tmp)
    min_tmp <- min(tmp)
    lymph_node_tiny_2[[paste0("Cluster", i, sep="")]]  <- (tmp[,1] - min(tmp))/(max_tmp - min_tmp)
}
plot_spatial_panel(lymph_node_tiny_2, metadata=paste0("Cluster", 1:4), ncol_layout=2,
                   guides='collect', pt_size=2.2, coord_flip=TRUE)
                   
plot_spatial_panel(lymph_node_tiny_2, gene=c('VPREB3', 'IGHG1', 'PRDX4', 
                                             'LTB', 'CCL20', 'LYVE1', 
                                             'IL7R', 'RGS9', 'MAPT'), 
                   ncol_layout=3,
                   pt_size=2, coord_flip=TRUE, 
                   panel_names=LETTERS[1:9], 
                   size_title = 10)

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