View source: R/Spatial_density_plot.R
Spatial_density_plot | R Documentation |
Plotting the contour density of selected cells or of all cells.
Spatial_density_plot( sample_names, bcs_merge, images_tibble, vgm_VDJ, title, size )
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. |
vgm_VDJ |
Data frame containing all the data on the cell. It must contain the column clonotype_id which describes the number of the clonotype to which the cell belongs. This data frame can be obtained by the assignment functions (VDJ_assignment_random_based, VDJ_assignment_density_based and VDJ_assignment_germline_based). |
title |
Character vector to name the plot. |
size |
Number, to define the size of the text, default = 15. |
Returns a plot of cell contour density on the spatial image.
## Not run: #Assignment density-based density_BCR_assignment<-Spatial_VDJ_assignment(GEX_matrix = GEX_matrix, vgm = vgm_with_simulated_VDJ, vgm_VDJ = vgm_with_simulated_VDJ$VDJ, celltype = "B", simulated_VDJ = simulated_B_cells_VDJ, method = "density") vgm_with_simulated_VDJ$VDJ<-density_BCR_assignment top_1_VDJ_BCR_density_data<-Spatial_selection_expanded_clonotypes( nb_clonotype = 1, vgm_VDJ = vgm_with_simulated_VDJ$VDJ) p_spatial_BCR_density_clonotype_density<-Spatial_density_plot( vgm_VDJ = top_1_VDJ_BCR_density_data, images_tibble = scaling_parameters[[5]], bcs_merge = scaling_parameters[[10]],sample_names = sample_names, title = "B cell density assignment") p_spatial_BCR_density_clonotype_density ## End(Not run)
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