plot_spatial_panel: A planel of XY scatter plots of Visium data with hexagonal...
In dputhier/dbfmcl: The scigenex package (Single-Cell Informative GENe Explorer)

plot_spatial_panel

R 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 Dec. 20, 2024, 1:59 a.m.