From 05288f024082e6bd96c4804057b200e8f2dc65c1 Mon Sep 17 00:00:00 2001
From: nicola-calonaci <nicola.calonaci@gmail.com>
Date: Wed, 7 Aug 2024 15:10:32 +0200
Subject: [PATCH] silent mode

---
 R/compute_posterior.R |  9 +++++----
 R/utils.R             | 12 +++++++-----
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/R/compute_posterior.R b/R/compute_posterior.R
index c7198af..b5c623a 100644
--- a/R/compute_posterior.R
+++ b/R/compute_posterior.R
@@ -34,7 +34,8 @@ compute_posterior = function(NV,
                          purity,
                          entropy_cutoff,
                          rho = 0.01,
-                         karyotypes)
+                         karyotypes,
+                         silent = FALSE)
 {
   NV_x = 1:DP
 
@@ -50,7 +51,7 @@ compute_posterior = function(NV,
       label = paste0(Major + minor, 'N (Mutated: ', p, "N)")
 
       if(is.data.frame(prior)){
-        if(!(label %in% prior$label)) cli::cli_alert_danger("Incomplete prior distribution!")
+        if(!(label %in% prior$label) & !silent) cli::cli_alert_danger("Incomplete prior distribution!")
         stopifnot(label %in% prior$label)
         prior = prior %>% dplyr::filter(label == !!label) %>% dplyr::pull(p)
       }
@@ -90,7 +91,7 @@ compute_posterior = function(NV,
   }
 
   if(is.na(purity)){
-    cli_alert_warning(text =
+    if(!silent) cli_alert_warning(text =
                         "With purity {.field {purity}} classification is not possible."
     )
     return(dplyr::tibble(ploidy = NA,
@@ -105,7 +106,7 @@ compute_posterior = function(NV,
   if (is.null(priors)){
     prior = 1
   } else {
-    prior = get_prior(priors, gene, tumor_type)
+    prior = get_prior(priors, gene, tumor_type, silent = silent)
   }
   posterior = lapply(karyotypes, function(k) {
     alleles = strsplit(k, split = ":")[[1]] %>% as.integer()
diff --git a/R/utils.R b/R/utils.R
index 99803d2..aaee142 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -199,14 +199,14 @@ get_gene_role = function(x, id){
 
 # Prior getter
 
-get_prior = function(x, gene, tumor_type){
+get_prior = function(x, gene, tumor_type, silent = FALSE){
 
-  if(is.null(x)) {
+  if(is.null(x) & !silent) {
     cli::cli_alert("No prior probabilities provided")
     return(1)
   }
 
-  if(!(gene %in% x$gene)) {
+  if(!(gene %in% x$gene) & !silent) {
     cli::cli_alert("No prior probability specified for {.field {gene}}")
     return(1)
   }
@@ -214,8 +214,10 @@ get_prior = function(x, gene, tumor_type){
   if(tumor_type %in% (x %>% dplyr::filter(gene == !!gene) %>% dplyr::pull(tumor_type))) {
     out = x %>% dplyr::filter(gene == !!gene, tumor_type == !!tumor_type)
   } else {
-    cli::cli_alert("No {.field {tumor_type}}-specific prior probability specified for {.field {gene}}")
-    cli::cli_alert("Using a pan-cancer prior")
+    if(!silent){
+      cli::cli_alert("No {.field {tumor_type}}-specific prior probability specified for {.field {gene}}")
+      cli::cli_alert("Using a pan-cancer prior")
+    }
     out = x %>% dplyr::filter(gene == !!gene, tumor_type == 'PANCA')
     }