Allows to select an area on the spatial image and to isolate the cells expressed on this part and repeat this process several times.

Spatial_selection_of_cells_on_image(
  vgm_VDJ,
  alpha,
  bcs_merge,
  images_tibble,
  sample_names,
  nbpoints,
  title,
  size,
  plotting
)

Arguments

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).
alpha: Number that give the transparency coefficient (value between 0 and 1). If it is not given it will automatically be 0.
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.
sample_names: Character vector containing the name of the sample.
nbpoints: Numerical value that limite the maximum number of mouse click for the selection, default = 100.
title: Character vector to name the plot.
size: Number, to define the size of the text, default = 15.
plotting: Character vector to return (TRUE) or not (FALSE) the plot of the selection

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 all the cells but the selected cells are distinguished. If plotting = FALSE it juste returns the dataframe.

Examples

if (FALSE) {
test<-Spatial_selection_of_cells_on_image(
vgm_VDJ = vgm_spatial_simulated$VDJ$B_cells$random_BCR_assignment,
images_tibble = scaling_parameters[[5]],
bcs_merge = scaling_parameters[[10]],sample_names = sample_names,
plotting = TRUE)
}