View source: R/Spatial_nb_SHM_compare_to_germline_plot.R
Spatial_nb_SHM_compare_to_germline_plot | R Documentation |
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 )
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. |
Spatial plot with cells colored by number of somatic hypermutation
## Not run: 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") ## End(Not run)
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