add documentation and NAMESPACE after adding Omnipath LR network plot…

… extension
saeyslab · Feb 27, 2024 · 8755605 · 8755605
1 parent 9412a5a
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Showing 3 changed files with 55 additions and 1 deletion.
diff --git a/NAMESPACE b/NAMESPACE
@@ -43,10 +43,12 @@ export(make_lr_target_prior_cor_heatmap)
 export(make_lr_target_scatter_plot)
 export(make_sample_lr_prod_activity_batch_plots)
 export(make_sample_lr_prod_activity_plots)
+export(make_sample_lr_prod_activity_plots_Omnipath)
 export(make_sample_lr_prod_plots)
 export(make_target_violin_plot)
 export(makenames_SCE)
 export(multi_nichenet_analysis)
+export(multi_nichenet_analysis_sampleAgnostic)
 export(p.adjust_empirical)
 export(perform_muscat_de_analysis)
 export(prioritize_condition_specific_receiver)

diff --git a/R/plotting.R b/R/plotting.R
@@ -503,7 +503,6 @@ make_sample_lr_prod_activity_plots_Omnipath = function(prioritization_tables, pr
   return(p)
 
 }
-
 #' @title make_sample_lr_prod_activity_batch_plots
 #'
 #' @description \code{make_sample_lr_prod_activity_batch_plots}  Visualize the scaled product of Ligand-Receptor (pseudobulk) expression per sample, and compare the different groups. In addition, show the NicheNet ligand activities in each receiver-celltype combination. On top of this summary plot, a heatmap indicates the batch value for each displayed sample.

diff --git a/man/make_sample_lr_prod_activity_plots_Omnipath.Rd b/man/make_sample_lr_prod_activity_plots_Omnipath.Rd
-Original file line number
+Diff line change
@@ Expand Up @@
       return(p)
     }
     #' @title make_sample_lr_prod_activity_batch_plots
     #'
     #' @description \code{make_sample_lr_prod_activity_batch_plots}  Visualize the scaled product of Ligand-Receptor (pseudobulk) expression per sample, and compare the different groups. In addition, show the NicheNet ligand activities in each receiver-celltype combination. On top of this summary plot, a heatmap indicates the batch value for each displayed sample.
@@ Expand Down @@