From e66b2d721554b3e7a6b6c8b18a9c84c53e23dd5c Mon Sep 17 00:00:00 2001
From: Giulio Caravagna <gcaravagn@gmail.com>
Date: Mon, 26 Oct 2020 12:50:17 +0100
Subject: [PATCH] Bug fix for automatic namings

---
 .DS_Store           | Bin 8196 -> 8196 bytes
 R/.DS_Store         | Bin 10244 -> 10244 bytes
 R/Clusters_denovo.R |  18 +++++++++++-------
 mobster.Rproj       |  17 +++++++++++++++++
 4 files changed, 28 insertions(+), 7 deletions(-)
 create mode 100644 mobster.Rproj

diff --git a/.DS_Store b/.DS_Store
index 85c7e67a9264d6b6ea5fa6ae601c5014bfc25441..82542db323fb3330208c5088afb33dace3fc92d1 100644
GIT binary patch
delta 40
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delta 238
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diff --git a/R/.DS_Store b/R/.DS_Store
index 822ae418b3ae20ac105a840b93cb0c8217ceb6ba..cc7baad54bfb0195bf7cbb359e66468bd821400f 100644
GIT binary patch
delta 37
tcmZn(XbG6$&#1I9U^hRb(q<k3QKrrDLMwPDHrQ=uSNO%U*<O^H835<R3yc5&

delta 61
zcmZn(XbG6$&#1gHU^hRb@@5_ZQ6^!21~-OGh7yK&21kZGAS;(4ak7D!)Fg41%_2fu
Qc{j5w{9@UBScI7w0OOnwt^fc4

diff --git a/R/Clusters_denovo.R b/R/Clusters_denovo.R
index 1bbfc56..ef24c09 100644
--- a/R/Clusters_denovo.R
+++ b/R/Clusters_denovo.R
@@ -27,26 +27,30 @@
 #' ggplot(new_assignments, aes(VAF, fill = cluster)) + geom_histogram(binwidth = 0.01)
 Clusters_denovo = function(x, y)
 {
-  is_mobster_fit(x)
-  is_mobster_input_dataset(y)
+  mobster:::is_mobster_fit(x)
+  mobster:::is_mobster_input_dataset(y)
   
   # actual clusters
   components = names(mobster:::.params_Pi(x))
   
   # per-component density
-  densities = NULL
+  densities = y
   for(component in seq_along(components))
   {
+    comp_density = ddbpmm(x, data = y$VAF, components = component, log = TRUE) %>% data.frame()
+    colnames(comp_density) = components[component]
+    
     densities = dplyr::bind_cols(
       densities,
-      ddbpmm(x, data = y$VAF, components = component, log = TRUE) %>% data.frame()
+      comp_density
     )
   }
-  colnames(densities) = components
+  # colnames(densities) = components
   densities = densities %>% as_tibble()
   
   # Hard clustering assignments
-  densities$cluster = components[apply(densities, 1, which.max)]
+  densities$cluster = components[apply(densities[, components, drop = FALSE], 1, which.max)]
   
-  dplyr::bind_cols(y, densities) %>% as_tibble()
+  densities
+  # dplyr::bind_cols(y, densities) %>% as_tibble()
 }
diff --git a/mobster.Rproj b/mobster.Rproj
new file mode 100644
index 0000000..21a4da0
--- /dev/null
+++ b/mobster.Rproj
@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source