Plotting a gene of interest in selected cells on the spatial image.

Spatial_marker_expression(
  sample_names,
  bcs_merge,
  images_tibble,
  matrix,
  marker,
  GEX_barcode,
  title,
  threshold,
  size
)

Arguments

sample_names: Character vector containing the name of the sample.
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.
matrix: Data frame containing all the genes detected per cells. This data frame can be obtained by the scaling_parameters functions.
marker: Character vector containing the name of a gene of interest.
GEX_barcode: Character vector containing the GEX barcode of the cell of interest with the -1 at the end
title: Character vector to name the plot.
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.
size: Number, to define the size of the text, default = 15.

Value

Returns a plot of the level of expression of a gene in cells.

Examples

if (FALSE) {
GEX_BCR_barcode<-vgm_with_simulated_VDJ$VDJ$GEX_barcode
GEX_BCR_barcode<-paste0(GEX_BCR_barcode,"-1") #Add -1 at the end of each barcode
#Without expression threshold
Spatial_marker_expression(matrix=scaling_parameters[[9]],
marker="CD3E",bcs_merge=scaling_parameters[[10]],
images_tibble=scaling_parameters[[5]],
GEX_barcode=GEX_BCR_barcode,sample_names=sample_names, title = "B cells",
threshold = "No")

#With expression threshold
Spatial_marker_expression(matrix=scaling_parameters[[9]],
marker="CD3E",bcs_merge=scaling_parameters[[10]],
images_tibble=scaling_parameters[[5]],
GEX_barcode=GEX_BCR_barcode,sample_names=sample_names, title = "B cells",
threshold = 5)
}