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

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.

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")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_2 was already loaded. 
load_example_dataset("7870305/files/lymph_node_tiny_clusters_2")
#> |-- INFO :  Dataset 7870305/files/lymph_node_tiny_clusters_2 was already loaded. 
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)
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 

                   
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)
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor. 
#> |-- INFO :  Feature is not a factor.