Plotting clusters of cells by choosing between 10X Genomics clustering or reclustering the cells.

Spatial_cluster(
  cluster = c("GEX_cluster", "reclustering"),
  GEX.out.directory.list,
  vgm_VDJ,
  vgm_cluster,
  sample_names,
  bcs_merge,
  images_tibble,
  title,
  size,
  legend_title
)

Arguments

cluster: Character vector to describe the clustering, "GEX_cluster" is for plotting 10X Genomics clustering and "reclustering" is for reclustering the cells according to the given subset.
GEX.out.directory.list: Character vector that give the path to filtered_feature_bc_matrix data.
vgm_VDJ: Data frame containing cell of interest and x and y coordinates and GEX_barcode.
vgm_cluster: Data frame containing GEX barcode and cluster given by 10X Genomics. Only needed if cluster parameter is set to "GEX_cluster".
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.
title: Character vector to name the plot.
size: Number, to define the size of the text, default = 15.
legend_title: Character vector to name the legend scale.

Value

If plotting = TRUE, returns a list containing [[1]] the plot of the selected cells according to their group, [[2]] a data frame that contains the column seurat_clusters with the new cluster. If plotting = FALSE, it returns just the data frame.

Examples

if (FALSE) {
#Clustering of whole cells regardless of cell type
GEX_cluster_B_cells<-Spatial_cluster(cluster = "GEX_cluster",
vgm_cluster = vgm_with_simulated_VDJ$spatial$cluster[[1]],
vgm_VDJ = vgm_with_simulated_VDJ$VDJ,
GEX.out.directory.list = GEX.out.directory.list[[1]],images_tibble=scaling_parameters[[5]],
bcs_merge=scaling_parameters[[10]], title = "B cells",
sample_names = sample_names, legend_title = "GEX clusters" )
GEX_cluster_B_cells[[1]]

#Reclustering with only B cells
reclustering_B_cells<-Spatial_cluster(cluster = "reclustering",
vgm_VDJ = vgm_with_simulated_VDJ$VDJ,
GEX.out.directory.list = GEX.out.directory.list[[1]],
images_tibble=scaling_parameters[[5]],bcs_merge=scaling_parameters[[10]],
title = "B cells", sample_names = sample_names, legend_title = "Reclustering")
reclustering_B_cells[[1]]
}