Plotting the expression of a gene module on the spatial image with or without a threshold.

Spatial_module_expression(
  sample_names,
  gene.set,
  GEX.out.directory.list,
  bcs_merge,
  images_tibble,
  title,
  size,
  threshold,
  legend_title
)

Arguments

sample_names: Character vector containing the name of the sample.
gene.set: Charcter vector containing the markers name.
GEX.out.directory.list: Character vector that give the path to filtered_feature_bc_matrix data.
bcs_merge: Data frame containing imagerow, imagecol and barcode of the cells belonging to the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 10.
images_tibble: Tbl-df containing the sample name, grob, height and width of the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 5.
title: Character vector to name the plot.
size: Number, to define the size of the text, default = 15.
threshold: Number, to define the threshold. If threshold = No, plot of the module and if threshold is a number, plot show the cells above the threshold.
legend_title: Character vector to name the legend scale.

Value

Returns a ggplot of gene module expression.

Examples

if (FALSE) {
gene.set <- list() # make empty list
gene.set[[1]] <- c("CD19","XBP1","SDC1") # put gene set in list

#Without expression threshold
Spatial_module_expression(sample_names = sample_names,gene.set = gene.set,
GEX.out.directory.list = GEX.out.directory.list[[1]],bcs_merge = scaling_parameters[[10]],
images_tibble = scaling_parameters[[5]], threshold = "No")

#With expression threshold
Spatial_module_expression(sample_names = sample_names,gene.set = gene.set,
GEX.out.directory.list = GEX.out.directory.list[[1]],bcs_merge = scaling_parameters[[10]],
images_tibble = scaling_parameters[[5]], threshold = 1)
}