View source: R/Spatial_VDJ_plot.R
Spatial_VDJ_plot | R Documentation |
Plotting immune repertoire data as clonotype or isotype for cells on a spatial image.
Spatial_VDJ_plot( sample_names, bcs_merge, images_tibble, title, size, legend_title, vgm_VDJ, analysis )
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. |
vgm_VDJ |
Data frame containing VDJ information, found in the vgm made by platypus. It must have x and y coordinates column and the column containing the factor to plot. |
analysis |
Column in the dataframe containing the factor of interest to plot on the spatial image. |
Returns a plot of the factor of interest express on a spatial image.
## Not run: Spatial_VDJ_plot(vgm_VDJ = top_5_VDJ_data,analysis = top_5_VDJ_data$VDJ_cgene, images_tibble = scaling_parameters[[5]], bcs_merge = scaling_parameters[[10]], sample_names = sample_names, title = "B cell", legend = "Isotype") ## End(Not run)
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