minor bugs

caravagnalab · Mar 15, 2024 · 3c6f87d · 3c6f87d
1 parent 40e8487
commit 3c6f87d
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Showing 16 changed files with 74 additions and 129 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,23 +1,15 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(plot,INCOMMON)
 S3method(print,INCOMMON)
 export(classification)
 export(classify)
 export(compute_posterior)
 export(init)
 export(parameters)
 export(plot_classification)
-export(plot_gene)
-export(plot_summary)
 export(posterior)
-import(CNAqc)
 import(cli)
 import(crayon)
-import(ggplot2)
-import(ggridges)
-import(ggsci)
-import(pheatmap)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)

diff --git a/R/classify.R b/R/classify.R
@@ -74,7 +74,7 @@ classify = function(x,
       purity = purity(x),
       entropy_cutoff = entropy_cutoff,
       rho = rho,
-      karyotypes = karyotypes,
+      karyotypes = karyotypes
     )
   })
 

diff --git a/R/compute_posterior.R b/R/compute_posterior.R
@@ -53,9 +53,11 @@ compute_posterior = function(NV,
       # Classification label
       label = paste0(Major + minor, 'N (Mutated: ', p, "N)")
 
-      if(!(label %in% priors$label)) cli::cli_alert_danger("Incomplete prior distribution!")
-      stopifnot(label %in% priors$label)
-      prior = prior %>% dplyr::filter(label == !!label) %>% dplyr::pull(p)
+      if(prior != 1){
+        if(!(label %in% priors$label)) cli::cli_alert_danger("Incomplete prior distribution!")
+        stopifnot(label %in% priors$label)
+        prior = prior %>% dplyr::filter(label == !!label) %>% dplyr::pull(p)
+      }
 
       # Expected VAF peak of mixture component
       expected_peak = expected_peaks[p]
@@ -136,4 +138,4 @@ compute_posterior = function(NV,
 
   return(posterior)
 }
-
+
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
 articles:
   Classify_Mutations: Classify_Mutations.html
   INCOMMON: INCOMMON.html
-last_built: 2024-03-15T18:52Z
+last_built: 2024-03-15T19:08Z
 urls:
   reference: caravagnalab.github.io/INCOMMON/reference
   article: caravagnalab.github.io/INCOMMON/articles

diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/man/classification.Rd b/man/classification.Rd
diff --git a/man/classify.Rd b/man/classify.Rd
diff --git a/man/compute_posterior.Rd b/man/compute_posterior.Rd
diff --git a/man/parameters.Rd b/man/parameters.Rd
diff --git a/man/plot.INCOMMON.Rd b/man/plot.INCOMMON.Rd
diff --git a/man/plot_classification.Rd b/man/plot_classification.Rd
diff --git a/man/plot_gene.Rd b/man/plot_gene.Rd
diff --git a/man/plot_summary.Rd b/man/plot_summary.Rd
diff --git a/man/posterior.Rd b/man/posterior.Rd
diff --git a/man/print.INCOMMON.Rd b/man/print.INCOMMON.Rd
diff --git a/vignettes/Classify_Mutations.Rmd b/vignettes/Classify_Mutations.Rmd
@@ -77,7 +77,7 @@ INCOMMON classification of a sample can be performed using function `classify`.
 ```{r}
 out = classify(
   x = input,
-  priors = pcawg_priors,
+  priors = NULL,
   entropy_cutoff = NULL,
   rho = 0.01
 )