updates to fix issue created by changes to ggtree

Author: gtonkinhill

.Rbuildignore

@@ -1,3 +1,4 @@
+^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 cran-comments.md

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rhierbaps
 Type: Package
 Title: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
-Version: 1.1.2
+Version: 1.1.3
 Authors@R: person("Gerry", "Tonkin-Hill", email = "g.tonkinhill@gmail.com", role = c("cre", "aut"))
 Description: Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) 
   algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences 
@@ -17,8 +17,9 @@ Imports:
     utils,
     ggplot2,
     gmp,
-    matrixStats
-RoxygenNote: 6.1.1
+    matrixStats,
+    patchwork
+RoxygenNote: 7.0.1
 Suggests: knitr,
     rmarkdown,
     ggtree,

NAMESPACE

@@ -4,3 +4,4 @@ export(hierBAPS)
 export(load_fasta)
 export(plot_sub_cluster)
 export(save_lml_logs)
+import(patchwork)

R/plot_sub_cluster.R

@@ -1,6 +1,8 @@
 #' plot_sub_cluster
 #'
 #' Creates a zoom plot using ggtree focusing on a cluster.
+#' 
+#' @import patchwork
 #'
 #'
 #' @param hb.object The resulting object from running hierBAPS
@@ -25,26 +27,27 @@ plot_sub_cluster <- function(hb.object, tree, level, sub.cluster){
   if ((!is.numeric(level)) || (level<1)) stop("Invalid level! Must be a positive integer.")
   if ((!is.numeric(sub.cluster)) || (sub.cluster<1)) stop("Invalid sub.cluster! Must be a positive integer.")
 
-
   level <- level+1
   if(!("ggtree" %in%
        rownames(utils::installed.packages()))) stop("This function requires ggtree to be installed")
 
   cluster.isolate <- hb.object$partition.df$Isolate[hb.object$partition.df[,level]==sub.cluster]
-
-  #Need to create a tempfile to supress the output of gzoom
-  ff <- tempfile()
-  grDevices::png(filename=ff)
-  gg2 <- ggtree::gzoom(tree, focus=which(tree$tip.label %in% cluster.isolate))
-  grDevices::dev.off()
-  unlink(ff)
-
+  
+  # Plot the full tree with the clade highlighted
+  hb.object$partition.df$is_in_cluster <- hb.object$partition.df$Isolate %in% cluster.isolate
+  full_tree <- ggtree::`%<+%`(ggtree::ggtree(tree), hb.object$partition.df) +
+    ggtree::geom_tippoint(ggplot2::aes_string(color="is_in_cluster"), size=0.5) +
+    ggplot2::theme(legend.position = "none") + 
+    ggplot2::scale_colour_manual(values=c("#000000", "#e31a1c"))
+  
+  # Subset the tree
   temp_column_id <- paste(c("factor(`level ", level, "`)"), collapse = "")
+  sub_tree <- ape::drop.tip(tree, tree$tip.label[!tree$tip.label %in% cluster.isolate])
+  sub_tree <- ggtree::`%<+%`(ggtree::ggtree(sub_tree), hb.object$partition.df) +
+    ggtree::geom_tippoint(ggplot2::aes_string(color=temp_column_id)) +
+    ggplot2::labs(color=temp_column_id) + 
+    ggplot2::theme(legend.position="right") +
+    ggplot2::scale_color_discrete(name=paste("level ", level, collapse = ""))
 
-  p2 <- gg2$p2
-  p2 <- ggtree::`%<+%`(p2, hb.object$partition.df)
-  p2 <- p2 + ggtree::geom_tippoint(ggplot2::aes_string(color=temp_column_id))
-  p2 <- p2+ ggplot2::labs(color=temp_column_id) + ggplot2::theme(legend.position="right") 
-
-  return(ggtree::multiplot(gg2$p1, p2, ncol = 2))
+  return(full_tree+sub_tree+patchwork::plot_layout(nrow = 1))
 }

README.Rmd

@@ -23,6 +23,8 @@ knitr::opts_chunk$set(
 
 # rhierbaps
 
+We have recently developed a faster verion of the BAPs clustering method. It can be found [here](https://github.com/gtonkinhill/fastbaps). 
+
 ## Installation
 `rhierbaps` is available on CRAN.
 ```{r, eval=FALSE}

README.md

@@ -5,6 +5,8 @@
 rhierbaps
 =========
 
+We have recently developed a faster verion of the BAPs clustering method. It can be found [here](https://github.com/gtonkinhill/fastbaps).
+
 Installation
 ------------
 
@@ -127,7 +129,7 @@ We can also check how long hierBAPS takes to run on the test dataset of 515 samp
 ``` r
 system.time(hierBAPS(snp.matrix, max.depth = 2, n.pops = 20, quiet = TRUE))
 #>    user  system elapsed 
-#>  79.411  12.454  98.874
+#>  89.755  10.111 117.755
 ```
 
 Plotting results
@@ -183,12 +185,10 @@ hb.results$lml.list
 #> -50858.92 
 #> 
 #> $`Depth 1`
-#>          1          2          3          4          5          6 
-#> -2121.8602 -4012.3594 -4237.7634 -3095.1866 -1525.7361 -3180.7573 
-#>          7          8          9         10         11         12 
-#> -4015.5022 -2104.5238 -1736.0193  -779.7693  -810.5962  -688.5221 
-#>         13 
-#>  -163.3203
+#>          1          2          3          4          5          6          7 
+#> -2121.8602 -4012.3594 -4237.7634 -3095.1866 -1525.7361 -3180.7573 -4015.5022 
+#>          8          9         10         11         12         13 
+#> -2104.5238 -1736.0193  -779.7693  -810.5962  -688.5221  -163.3203
 ```
 
 Caculating assignment probabilities

cran-comments.md

@@ -1,11 +1,21 @@
 ## Resubmission
 This is a an updated version. In this version I have:
 
+* Fixed an error cause by changes to the ggtree plotting package
+
+## Resubmission
+This is a an updated version. In this version I have:
+
+* Fixed a bug that caused the  algorithm to stop prematurely on large alignments
+
+## Resubmission
+This is a an updated version. In this version I have:
+
 * Fixed a minor bug that caused an error when a cluster contained only a single SNP
 * Added functionality to accept an ape DNAbin object
 
 ## Test environments
-* local OS X install, R 3.5.0
+* local OS X install, R 3.6.1
 * ubuntu 14.04 (on travis-ci), R 3.5.0
 * win-builder (devel and release)