From e5517fb03edd5664503c85c83e68c0643a036a3c Mon Sep 17 00:00:00 2001
From: Alex White <aewhite100@gmail.com>
Date: Tue, 28 Feb 2017 10:49:14 -0500
Subject: [PATCH 1/2] .DS_Store banished!

---
 data/.DS_Store      | Bin 6148 -> 0 bytes
 vignettes/.DS_Store | Bin 6148 -> 0 bytes
 2 files changed, 0 insertions(+), 0 deletions(-)
 delete mode 100644 data/.DS_Store
 delete mode 100644 vignettes/.DS_Store

diff --git a/data/.DS_Store b/data/.DS_Store
deleted file mode 100644
index 9384f9df5bca33195a56035d4a8902c5ffdc766c..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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diff --git a/vignettes/.DS_Store b/vignettes/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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From 841082b68c59582ccb35d574b7333d415f1bb413 Mon Sep 17 00:00:00 2001
From: Alex White <aewhite100@gmail.com>
Date: Thu, 2 Mar 2017 13:09:05 -0500
Subject: [PATCH 2/2] Changes made to TopicMetaDiversity.R to enhance
 flexibility.

---
 R/TopicMetaDiversity.R | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/R/TopicMetaDiversity.R b/R/TopicMetaDiversity.R
index 52306c5..bbe59a7 100644
--- a/R/TopicMetaDiversity.R
+++ b/R/TopicMetaDiversity.R
@@ -13,6 +13,9 @@
 #'               \item{\code{y2d}}{ a N-1 vector of distances between adjacent sites plotted as segments connecting the two sites}
 #'           }
 #'
+#'  @param  y2d.type The type of comparison for y2d. Function will calculate the mean and difference 
+#'                   between adjacent sites when given raw values, or will plot the simply plot the values provides
+#'                   in y2d vector privided.  Can be one of "raw", "mean", or "diff". Defaults to "diff".    
 #'  @param  margin  The values of the margin on the bottom, left, top and right.
 #'  @param  col.pts The color of the points for \code{annotation$y}.
 #'  @param  pch.pts The size of the points. Defaults to 20.
@@ -53,6 +56,7 @@
 
 
 TopicMetaDiversity = function(annotation,
+                              y2d.type = c("diff"),
                               margin=c(5,5,2,5),
                               col.pts = "red3",
                               pch.pts=20,
@@ -73,6 +77,21 @@ TopicMetaDiversity = function(annotation,
                               line.y2d=3,
                               round_off=0,
                               legend.pos="topleft"){
+  if(y2d.type=="diff"){
+    diff.mat <- t(outer(annotation$y2d, annotation$y2d, `-`)) 
+    rownames(diff.mat) <- annotation$x_names
+    colnames(diff.mat) <- annotation$x_names
+    diff.order <- as.vector(annotation$x_names[order(annotation$y2d, annotation$x_names, decreasing =F)])
+    diff.mat <- diff.mat[diff.order,diff.order]
+    annotation$y2d <- c(abs(split(diff.mat, (row(diff.mat) - col(diff.mat)))$"1"),0)
+    
+  }
+  if(y2d.type=="mean"){
+    annotation$y2d<-c(((annotation$y2d[1:(length(annotation$y2d)-1)]+annotation$y2d[-1])/2),0)
+  }
+  if(y2d.type=="raw"){
+    annotation$y2d<-annotation$y2d
+  }
 
 if(is.null(ylim)){
  par(mar = margin)