Plotting number of somatic hypermutation of clones compare to the germline sequence of the clonotype.

Spatial_nb_SHM_compare_to_germline_plot(
  simulation = c(TRUE, FALSE),
  vgm_VDJ,
  AbForest_output,
  nb_clonotype,
  simulated_VDJ,
  sample_names,
  bcs_merge,
  images_tibble,
  title,
  size,
  legend_title
)

Arguments

simulation: Logical operator, to describe which type of data we want to plot, TRUE if the data are output of Echidna simulation and FALSE if the we use real dataset.
vgm_VDJ: Data frame containing cell of interest and x and y coordinates and GEX_barcode.
AbForest_output: Igraph of phylogenetic tree of a clonotype of interest found in the large list output from AntibodyForest function, only needed if we use real dataset.
nb_clonotype: Numeric, value which designates the clonotype we want to study if we use simulated data (Echidna output).
simulated_VDJ: Large list, output of Echidna simulate_repertoire function. Only needed if we use simulated data.
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

Spatial plot with cells colored by number of somatic hypermutation

Examples

if (FALSE) {
Spatial_nb_SHM_compare_to_germline_plot(simulation = FALSE,
AbForest_output=forest[[1]][[2]], vgm_VDJ = vgm$VDJ,
images_tibble = scaling_parameters[[5]],bcs_merge = scaling_parameters[[10]],
sample_names = sample_names,
title = "Number of SHM of clonotype 10", legend_title = "nb of SHM")
}