Merge pull request #19 from KarchinLab/pictograph2

update tool

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pictograph
 Title: Tools for modeling clonal evolution of a cancer
-Version: 1.2.1.1
+Version: 1.3.0
 Authors@R: 
     person(given = "Jiaying",
            family = "Lai",
@@ -15,13 +15,19 @@ Suggests:
     testthat,
     knitr,
     rmarkdown
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Imports: 
-    igraph,
     ggplot2,
-    tidyr,
-    dplyr,
     rjags,
-    ggmcmc,
-    stringr
+    stringr,
+    readr (>= 2.1.4),
+    tidyverse (>= 2.0.0),
+    dplyr (>= 1.1.1),
+    tidyr (>= 1.3.0),
+    LaplacesDemon (>= 16.1.6),
+    igraph (>= 2.0.1),
+    viridis (>= 0.6.5),
+    ggmcmc (>= 1.5.1),
+    UpSetR (>= 1.4.0),
+    cluster (>= 2.1.6)

NAMESPACE

@@ -1,37 +1,44 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(mutate,admat)
+S3method(mutate,admat.2)
+S3method(mutate,admat.3)
+S3method(mutate,column)
+S3method(mutate,n.columns)
+S3method(mutate,n.columns.clusterprob)
 export(calcSubcloneProportions)
-export(calcSubcloneProportions2)
 export(calcTreeScores)
-export(clusterSep)
+export(calculateTreeScoreMutations)
 export(collectBestKChains)
 export(colorScheme)
-export(enumerateSpanningTrees)
 export(enumerateSpanningTreesModified)
-export(estimateCCFs)
 export(estimateClusterAssignments)
+export(estimateICN)
+export(estimateMCFs)
+export(estimateMultiplicity)
+export(estimateMultiplicityMatrix)
 export(filterEdgesBasedOnCCFs)
-export(forceCCFs)
 export(generateAllTrees)
-export(importCSV)
+export(importFiles)
+export(mcmcMain)
 export(mergeSetChains)
-export(plotAllZProb)
-export(plotBIC)
-export(plotCCFViolin)
-export(plotChainsCCF)
-export(plotClusterAssignmentProb)
+export(plotChainsMCF)
 export(plotClusterAssignmentProbVertical)
-export(plotDensityCCF)
 export(plotEnsembleTree)
-export(plotPPD)
+export(plotMCFViolin)
 export(plotSubcloneBar)
 export(plotSubclonePie)
 export(plotTree)
 export(prepareGraph)
-export(prepareGraphForGabowMyers)
+export(runMCMCForAllBoxes)
+export(separateMutationsBySamplePresence)
 export(writeClusterAssignmentsTable)
-export(writeClusterCCFsTable)
+export(writeClusterMCFsTable)
+export(writeIcnTable)
+export(writeMultiplicityTable)
 export(writeSetKTable)
+import(UpSetR)
+import(cluster)
 import(dplyr)
 import(ggmcmc)
 import(ggplot2)
@@ -40,13 +47,10 @@ import(magrittr)
 import(methods)
 import(readr)
 import(rjags)
+import(stringr)
 import(tibble)
 import(tidyr)
+import(tidyverse)
+import(viridis)
 importFrom(epiR,epi.betabuster)
-importFrom(ggmcmc,ggs)
-importFrom(magrittr,set_colnames)
 importFrom(stringr,str_replace)
-importFrom(stringr,str_replace_all)
-importFrom(tidyr,pivot_longer)
-importFrom(tidyr,unite)
-importFrom(viridis,viridis)