Ordev

InfoAndInputs/.gitignore

@@ -0,0 +1 @@
+.DS_Store

phyloscannerR/.gitignore

@@ -1,3 +1,4 @@
 .Rproj.user
 .Rhistory
 .RData
+.DS_Store

phyloscannerR/DESCRIPTION

@@ -4,7 +4,7 @@ Version: 1.8.0
 Authors@R: c(person("Matthew", "Hall", email = "[email protected]", role = c("aut", "cre")), person("Chris", "Wymant", email = "[email protected]", role = c("aut")), person("Oliver", "Ratmann", email = "[email protected]", role = c("aut")))
 Description: An R package for the second half of phyloscanner (tree analysis).
 Depends: R (>= 3.4.0)
-Imports: ape, argparse, extraDistr, ff, GGally, ggtree, grid, gtable, kimisc, network, pegas, phangorn, phytools, prodlim, RColorBrewer, reshape2, scales, sna, tidyverse, treeio (>= 1.6.2), viridis
+Imports: ape, argparse, extraDistr, ff, GGally, ggtree, grid, gtable, kimisc, network, pegas, phangorn, phytools, prodlim, RColorBrewer, reshape2, RBGL, scales, sna, tidyverse, treeio (>= 1.6.2), viridis
 License: GPL
 Encoding: UTF-8
 LazyData: true

phyloscannerR/NAMESPACE

@@ -54,11 +54,14 @@ export(downsample.host)
 export(downsample.tree)
 export(draw.summary.statistics)
 export(drop.tip.get.map)
+export(extract.subgraph)
 export(extract.subtrees.for.hosts)
 export(extract.tt.subgraph)
 export(find.bam.and.references)
 export(find.duplicate.tips)
 export(find.gaps)
+export(find.networks)
+export(find.pairs.in.networks)
 export(form.rectangles)
 export(gather.summary.statistics)
 export(get.ancestral.sequence)
@@ -110,6 +113,9 @@ export(phyloscanner.analyse.tree)
 export(phyloscanner.analyse.trees)
 export(phyloscanner.generate.blacklist)
 export(phyloscanner.reconstruct)
+export(phyloscanner.to.simmap)
+export(plot.chain)
+export(plot.network)
 export(prepare.tree)
 export(process.tree)
 export(produce.host.graphs)
@@ -127,6 +133,7 @@ export(reconstruct.host.ancestral.sequences)
 export(rename.blacklisted.tips)
 export(resolve.tree.into.host.clades)
 export(select.windows.by.read.and.tip.count)
+export(simmap.to.phyloscanner)
 export(simplified.transmission.summary)
 export(simplify.summary)
 export(simplify.summary.multinomial)
@@ -141,9 +148,12 @@ export(transmission.summary)
 export(write.ann.nexus)
 export(write.ann.tree)
 export(write.annotated.tree)
+import(GGally)
 import(RColorBrewer)
 import(dplyr)
 import(ggplot2)
+import(ggtree)
+import(glue)
 import(grid)
 import(gtable)
 import(purrr)
@@ -152,6 +162,7 @@ import(tidyr)
 import(tidyverse)
 import(viridis)
 importFrom(GGally,ggnet2)
+importFrom(RBGL,edmondsOptimumBranching)
 importFrom(ape,.compressTipLabel)
 importFrom(ape,.uncompressTipLabel)
 importFrom(ape,as.DNAbin)
@@ -175,7 +186,11 @@ importFrom(ggtree,geom_point2)
 importFrom(ggtree,geom_tiplab)
 importFrom(ggtree,geom_treescale)
 importFrom(ggtree,ggtree)
+importFrom(igraph,clusters)
+importFrom(igraph,graph.data.frame)
+importFrom(igraph,igraph.to.graphNEL)
 importFrom(network,as.network.matrix)
+importFrom(network,network)
 importFrom(phangorn,Ancestors)
 importFrom(phangorn,Children)
 importFrom(phangorn,Descendants)
@@ -188,6 +203,7 @@ importFrom(phangorn,phyDat2alignment)
 importFrom(phangorn,pml)
 importFrom(phytools,nodeheight)
 importFrom(readr,read_csv)
+importFrom(reshape2,dcast)
 importFrom(reshape2,melt)
 importFrom(scales,pretty_breaks)
 importFrom(tibble,as.tibble)

phyloscannerR/R/main_analysis.R

@@ -628,6 +628,7 @@ blacklist <- function(ptrees,
 #' @importFrom tidyr unnest
 #' @importFrom phangorn Ancestors Descendants Children mrca.phylo getRoot
 #' @export phyloscanner.analyse.trees 
+#' @seealso \code{\link{find.pairs.in.networks}}, \code{\link{find.networks}}
 #' @example inst/example/ex.phyloscanner.analyse.trees.R
 #' 
 phyloscanner.analyse.trees <- function(
@@ -1253,7 +1254,7 @@ multipage.summary.statistics <- function(ptrees, sum.stats, hosts = all.hosts.fr
 #' @import ggplot2
 #' @export write.annotated.tree
 
-write.annotated.tree <- function(ptree, file.name, format = c("pdf", "nex"), pdf.scale.bar.width = 0.01, pdf.w = 50, pdf.hm = 0.15, verbose = F){
+write.annotated.tree <- function(ptree, file.name, format = c("pdf", "nex", "ggplot"), tree.colours=NULL, pdf.scale.bar.width = 0.01, pdf.w = 50, pdf.hm = 0.15, verbose = F){
   tree <- ptree$tree
   read.counts <- ptree$read.counts
 
@@ -1266,12 +1267,26 @@ write.annotated.tree <- function(ptree, file.name, format = c("pdf", "nex"), pdf
 
   if(verbose) cat(paste0("Writing .",format," tree to file ",file.name,"\n"))
 
-  if(format == "pdf"){
+  if(!format %in% c("pdf","nex","ggplot")){
+	  stop("Unknown tree output format")
+  }
+
+  if(format == "nex"){
+	  write.ann.nexus(tree, file=file.name, annotations = c("INDIVIDUAL", "SPLIT", "READ_COUNT"))
+  }
+
+  if(is.null(tree.colours)){
+	hue.pal <- scales:::hue_pal(h= c(0, 360) + 15, c = 100, l = 65, h.start = 0, direction = 1)	  
+	tree.colours <- hue.pal(length(levels(attr(tree,'INDIVIDUAL'))))
+	names(tree.colours) <- levels(attr(tree,'INDIVIDUAL'))	  
+  }
+
+  if(format %in% c("pdf","ggplot")){
 
-    tree.display <- ggtree(tree, aes(color=BRANCH_COLOURS)) +
+	tree.display <- ggtree(tree, aes(color=BRANCH_COLOURS)) +
       geom_point2(aes(subset=SUBGRAPH_MRCA, color=INDIVIDUAL), shape = 23, size = 3, fill="white") +
       geom_point2(aes(color=INDIVIDUAL, shape=BLACKLISTED), size=1) +
-      scale_color_hue(na.value = "black", drop=F) +
+      scale_color_manual(values=tree.colours, na.value = "black", drop=F) +
       scale_shape_manual(values=c(16, 4)) +
       theme(legend.position="none") +
       geom_tiplab(aes(col=INDIVIDUAL)) +
@@ -1296,12 +1311,14 @@ write.annotated.tree <- function(ptree, file.name, format = c("pdf", "nex"), pdf
 
     tree.display <- tree.display + ggplot2::xlim(0, 1.1*x.max)
     tree.display
-    ggsave(file.name, device="pdf", height = pdf.hm*length(tree$tip.label), width = pdf.w, limitsize = F)
-
-  } else if(format == "nex"){
-    write.ann.nexus(tree, file=file.name, annotations = c("INDIVIDUAL", "SPLIT", "READ_COUNT"))
-  } else {
-    stop("Unknown tree output format")
+  }
+
+  if(format == "pdf"){
+    ggsave(file.name, device="pdf", height = pdf.hm*length(tree$tip.label), width = pdf.w, limitsize = F)    
+  } 
+
+  if(format == "ggplot"){
+	return(tree.display)
   }
 }
 

phyloscannerR/R/parsimony_reconstruction_methods.R

@@ -153,7 +153,7 @@ split.hosts.to.subgraphs <- function(tree,
   rs.subgraphs <- rs.subgraphs %>%
     mutate(host = map_chr(subgraph, function(x) unlist(strsplit(x, "-SPLIT"))[1]),
            tip = map(subgraph, function(x) tree$tip.label[results$split.tips[[x]]])) %>%
-    unnest() %>%
+    unnest(c(host, subgraph, tip)) %>%
     select(host, subgraph, tip)
 
   list(tree=tree, rs.subgraphs=rs.subgraphs)