version 1.1.8

cran · Dec 18, 2019 · 5e4fbe3 · 5e4fbe3
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,15 +1,15 @@
 Package: MetaLonDA
 Type: Package
 Title: Metagenomics Longitudinal Differential Abundance Method
-Version: 1.1.5
-Date: 2019-04-12
+Version: 1.1.8
+Date: 2019-12-17
 Author: Ahmed A. Metwally, Yang Dai, Patricia W. Finn, David L. Perkins
 Maintainer: Ahmed A. Metwally <ametwall@stanford.edu>
 URL: https://github.com/aametwally/MetaLonDA
 BugReports: https://github.com/aametwally/MetaLonDA/issues
 Description: Identify time intervals of differentially abundant metagenomic features in longitudinal studies (Metwally AA, et al., Microbiome, 2018 <doi:10.1186/s40168-018-0402-y>).
 License: MIT + file LICENSE
-Depends: R(>= 3.2.0)
+Depends: R(>= 3.5.0)
 Imports: gss, plyr, zoo, pracma, ggplot2, parallel, doParallel,
         metagenomeSeq, DESeq2, edgeR
 Suggests: knitr, rmarkdown
@@ -18,7 +18,7 @@ Repository: CRAN
 NeedsCompilation: no
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 VignetteBuilder: knitr
-Packaged: 2019-04-13 09:02:39 UTC; ahmedmetwally
-Date/Publication: 2019-04-13 22:43:03 UTC
+Packaged: 2019-12-17 20:11:48 UTC; ahmedmetwally
+Date/Publication: 2019-12-18 02:10:26 UTC
diff --git a/MD5 b/MD5
@@ -1,31 +1,31 @@
-f1d29a4e28e77cd66a1e4269e731170a *DESCRIPTION
+9d448f5402dbd707d92d3356f9d52bb4 *DESCRIPTION
 87427359a7b5eb6dd3ab20040a09bc94 *LICENSE
 d1b67c5499f5614714b98da640a55229 *NAMESPACE
 06f7d7f8740c6b69bae04c2b6a060699 *R/CurveFitting.R
-742d3248c7cbf5bc6acb37f830d167e0 *R/Metalonda.R
+1c491ffcad8f16bbcbb1288037b5dbb8 *R/Metalonda.R
 30430f68040d21ccd131224e8c29d02f *R/Normalization.R
 3d2a91bfa01b5f9912ebdd42e6ea4d35 *R/Permutation.R
-c4866b6d4b309f6e96acc5b97562b549 *R/Visualization.R
+bbaeb396927f5f6926bf6038fbbaa327 *R/Visualization.R
 0fef69ca0c788e0859225bf769872997 *R/metalonda_test_data.R
-f24421b005eded754e55adf445b99bb5 *build/vignette.rds
+05400e885dffd157b3583b427bf42223 *build/vignette.rds
 173a19ff73e64e4126b88c5c54164993 *data/metalonda_test_data.RData
 7bfc565366a6d32316994cb277334668 *inst/CITATION
 c32dc4061782f1fc96909da90a3ce517 *inst/doc/MetaLonDA.R
 528fcddfc425fcdc4b940b49f7e6be6a *inst/doc/MetaLonDA.Rmd
-707a1a69cb59ee8361d10704b5121ec7 *inst/doc/MetaLonDA.html
+251721d70f61873097aba5f061ce44f3 *inst/doc/MetaLonDA.html
 fa9ed6d6cd4ede7a7123c55b59d35bb4 *man/areaPermutation.Rd
 aedacebd46c1cced168845b45e5f4398 *man/curveFitting.Rd
 b4e1f0f5fb579486ef40e69cb382a759 *man/findSigInterval.Rd
 c179893611cb8d9d94c7d1710af7ab03 *man/intervalArea.Rd
-3bd94faa48cf441bac07baa77b1a863f *man/metalonda.Rd
-8c5d28fa098fef5d08d469fa2b668009 *man/metalondaAll.Rd
+ad06965cc24b84b6283e9141f32cb0aa *man/metalonda.Rd
+bcf6964c2dcc3e46f9df9f833701f445 *man/metalondaAll.Rd
 e674c6406d9945d6b63e471aee4fdba5 *man/metalonda_test_data.Rd
 412a3fc87c485194eb59f08c6ab01f5b *man/normalize.Rd
-a972eb5d64d1c632551945a5bed7afbd *man/permutation.Rd
+bcbaf706a9013033a748c079022fcd32 *man/permutation.Rd
 51ddf6834e284bcd0d00da20863e7558 *man/visualizeARHistogram.Rd
-1210491d39dfa77209a13239ec6a9e02 *man/visualizeArea.Rd
-07a57f4a1baafe594f1a88bea530126e *man/visualizeFeature.Rd
-10537b29e7489524ab651cd2450f581c *man/visualizeFeatureSpline.Rd
-58c3c2ca7b2ae890a3060ae6fed36254 *man/visualizeTimeIntervals.Rd
+80a32b082b01b3ef1b90d93cbd9e9550 *man/visualizeArea.Rd
+79e7db6264970ad9263337ecb306783c *man/visualizeFeature.Rd
+047d016416f279da3a620ece3b181365 *man/visualizeFeatureSpline.Rd
+0f2bfa3b5393b31bfe7ac7405b23c23a *man/visualizeTimeIntervals.Rd
 807f0038a0f932a92f4469a67d704486 *man/visualizeVolcanoPlot.Rd
 528fcddfc425fcdc4b940b49f7e6be6a *vignettes/MetaLonDA.Rmd
diff --git a/R/Metalonda.R b/R/Metalonda.R
@@ -158,7 +158,7 @@ metalonda = function(Count, Time, Group, ID, n.perm = 500, fit.method = "nbinomi
     visualizeArea(aggregate.df, model, fit.method, st, en, text, group.levels, unit = time.unit, ylabel = ylabel,
                   col = col, prefix = prefix)
   }
-
+   
 
   ## Calculate start, end, dominant for each interval
   interval.start = points[-length(points)]

diff --git a/R/Visualization.R b/R/Visualization.R
@@ -16,7 +16,8 @@
 #' Ahmed Metwally (ametwall@stanford.edu)
 #' @examples 
 #' data(metalonda_test_data)
-#' dir.create(file.path("Test"))
+#' pfx = tempfile()
+#' dir.create(file.path(pfx))
 #' n.sample = 5
 #' n.timepoints = 10
 #' n.group = 2
@@ -25,7 +26,8 @@
 #' ID = factor(rep(1:(2*n.sample), each = n.timepoints))
 #' points = seq(1, 10, length.out = 10)
 #' aggregate.df = data.frame(Count = metalonda_test_data[1,], Time = Time, Group = Group, ID = ID)
-#' visualizeFeature(aggregate.df, text = rownames(metalonda_test_data)[1], Group)
+#' visualizeFeature(df = aggregate.df, text = rownames(metalonda_test_data)[1], 
+#' group.levels = Group, prefix = pfx)
 #' @export
 visualizeFeature = function (df, text, group.levels, unit = "days", ylabel = "Normalized Count", 
                              col = c("blue", "firebrick"), prefix = "Test")
@@ -142,7 +144,7 @@ visualizeArea = function(aggregate.df, model.ss, method, start, end, text, group
     sub.11[[i]] = subset(model.ss$dd.1, Time >= start[i] & Time <= end[i])  
     sub.10[[i]] = subset(model.ss$dd.0, Time >= start[i] & Time <= end[i])
     cmd = sprintf('geom_ribbon(data=sub.10[[%d]], aes(ymin = sub.11[[%d]]$Count, ymax = Count), colour= "grey3", fill="grey69", 
-                  alpha = "0.6")', i, i)
+                  alpha = 0.6)', i, i)
     if (i != 1)
     {
       xx = paste(xx, cmd, sep = "+")

diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/inst/doc/MetaLonDA.html b/inst/doc/MetaLonDA.html
@@ -7,12 +7,13 @@
 <meta charset="utf-8" />
 <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 <meta name="generator" content="pandoc" />
+<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
 
 <meta name="viewport" content="width=device-width, initial-scale=1">
 
 <meta name="author" content="Ahmed A. Metwally" />
 
-<meta name="date" content="2019-04-13" />
+<meta name="date" content="2019-12-17" />
 
 <title>An Introduction to the MetaLonDA Package</title>
 
@@ -70,7 +71,7 @@
       if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue;
       var style = rule.style.cssText;
       // check if color or background-color is set
-      if (rule.style.color === '' || rule.style.backgroundColor === '') continue;
+      if (rule.style.color === '' && rule.style.backgroundColor === '') continue;
       // replace div.sourceCode by a pre.sourceCode rule
       sheets[i].deleteRule(j);
       sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
@@ -95,7 +96,7 @@
 
 <h1 class="title toc-ignore">An Introduction to the MetaLonDA Package</h1>
 <h4 class="author">Ahmed A. Metwally</h4>
-<h4 class="date">2019-04-13</h4>
+<h4 class="date">2019-12-17</h4>
 
 
 
@@ -652,6 +653,9 @@ <h2>Bugs and Suggestions</h2>
 
 
 
+<!-- code folding -->
+
+
 <!-- dynamically load mathjax for compatibility with self-contained -->
 <script>
   (function () {

diff --git a/man/metalonda.Rd b/man/metalonda.Rd
diff --git a/man/metalondaAll.Rd b/man/metalondaAll.Rd
diff --git a/man/permutation.Rd b/man/permutation.Rd
diff --git a/man/visualizeArea.Rd b/man/visualizeArea.Rd
diff --git a/man/visualizeFeature.Rd b/man/visualizeFeature.Rd
diff --git a/man/visualizeFeatureSpline.Rd b/man/visualizeFeatureSpline.Rd
diff --git a/man/visualizeTimeIntervals.Rd b/man/visualizeTimeIntervals.Rd