[med-svn] [r-bioc-biomformat] 01/05: New upstream version 1.6.0
Andreas Tille
tille at debian.org
Fri Nov 10 07:53:23 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-bioc-biomformat.
commit afd33541b850728b9597b9e8085e9b2ab8079808
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 10 08:50:10 2017 +0100
New upstream version 1.6.0
---
DESCRIPTION | 4 +-
build/vignette.rds | Bin 218 -> 219 bytes
inst/doc/biomformat.R | 18 +++---
inst/doc/biomformat.html | 140 +++++++++++++++++++++++++++++++++++++++--------
4 files changed, 129 insertions(+), 33 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b11bdf2..0ede763 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: biomformat
-Version: 1.4.0
+Version: 1.6.0
Date: 2016-04-16
Maintainer: Paul J. McMurdie <mcmurdie at stanford.edu>
License: GPL-2
@@ -22,4 +22,4 @@ Collate: 'allClasses.R' 'allPackage.R' 'IO-methods.R' 'BIOM-class.R'
'validity-methods.R'
biocViews: DataImport, Metagenomics, Microbiome
NeedsCompilation: no
-Packaged: 2017-04-25 00:27:37 UTC; biocbuild
+Packaged: 2017-10-31 00:35:43 UTC; biocbuild
diff --git a/build/vignette.rds b/build/vignette.rds
index 707a6db..2104f83 100644
Binary files a/build/vignette.rds and b/build/vignette.rds differ
diff --git a/inst/doc/biomformat.R b/inst/doc/biomformat.R
index 5b39267..7f1c020 100644
--- a/inst/doc/biomformat.R
+++ b/inst/doc/biomformat.R
@@ -1,7 +1,7 @@
-## ----packages------------------------------------------------------------
+## ----packages--------------------------------------------------------------
library("biomformat"); packageVersion("biomformat")
-## ----read-biom-examples--------------------------------------------------
+## ----read-biom-examples----------------------------------------------------
min_dense_file = system.file("extdata", "min_dense_otu_table.biom",
package = "biomformat")
min_sparse_file = system.file("extdata", "min_sparse_otu_table.biom",
@@ -21,39 +21,39 @@ x5 = read_biom(rich_dense_char)
x6 = read_biom(rich_sparse_char)
x1
-## ----accessor-examples-table---------------------------------------------
+## ----accessor-examples-table-----------------------------------------------
biom_data(x1)
biom_data(x2)
-## ----matrix-coercion-----------------------------------------------------
+## ----matrix-coercion-------------------------------------------------------
as(biom_data(x2), "matrix")
-## ----observ-meta---------------------------------------------------------
+## ----observ-meta-----------------------------------------------------------
observation_metadata(x1)
observation_metadata(x2)
observation_metadata(x3)
observation_metadata(x4)[1:2, 1:3]
class(observation_metadata(x4))
-## ----plot-examples-------------------------------------------------------
+## ----plot-examples---------------------------------------------------------
sample_metadata(x1)
sample_metadata(x2)
sample_metadata(x3)
sample_metadata(x4)[1:2, 1:3]
class(sample_metadata(x4))
-## ----plot----------------------------------------------------------------
+## ----plot------------------------------------------------------------------
plot(biom_data(x4))
boxplot(as(biom_data(x4), "vector"))
heatmap(as(biom_data(x4), "matrix"))
-## ----write-biom-examples-------------------------------------------------
+## ----write-biom-examples---------------------------------------------------
outfile = tempfile()
write_biom(x4, outfile)
y = read_biom(outfile)
identical(x4, y)
-## ----compare-files-diff, eval=FALSE--------------------------------------
+## ----compare-files-diff, eval=FALSE----------------------------------------
# # On Unix OSes
# system(paste0("diff ", rich_sparse_file, outfile))
# # On windows
diff --git a/inst/doc/biomformat.html b/inst/doc/biomformat.html
index 1a8c72d..3b92b9e 100644
--- a/inst/doc/biomformat.html
+++ b/inst/doc/biomformat.html
@@ -4,23 +4,30 @@
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<title>The biomformat package vignette</title>
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+
+<h1 class="title toc-ignore">The biomformat package vignette</h1>
+<p class="author-name">Paul J. McMurdie</p>
+<h4 class="date"><em>30 October 2017</em></h4>
-<div id="header">
-<h1 class="title">The biomformat package vignette</h1>
-<h4 class="author"><em>Paul J. McMurdie</em></h4>
</div>
<h1>Contents</h1>
@@ -78,9 +145,9 @@ document.addEventListener("DOMContentLoaded", function() {
<p>This is an <a href="http://www.rstudio.com/ide/docs/r_markdown">R Markdown document</a>. Markdown is a simple formatting syntax for authoring web pages. Further details on <a href="http://www.rstudio.com/ide/docs/r_markdown">R markdown here</a>.</p>
<p>The BIOM file format (canonically pronounced “biome”) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for <a href="http://www.earthmicrobiome.org/">the Earth Microbiome Project</a> and is a <a href="http://gensc.org/">Genomics Standards Consortium</a> candidate project. Please see <a href="http://biom-format.org/">the biom-format home page</a> for more details.</p>
<p>This demo is designed to provide an overview of the biom package to get you started using it quickly. The biom package itself is intended to be a utility package that will be depended-upon by other packages in the future. It provides I/O functionality, and functions to make it easier to with data from biom-format files. It does not (and probably should not) provide statistical analysis functions. However, it does provide tools to access data from BIOM format files in ways that are ext [...]
-<p><strong>Package versions</strong> at the time (Mon Apr 24 20:27:33 2017) of this build:</p>
+<p><strong>Package versions</strong> at the time (Mon Oct 30 20:35:37 2017) of this build:</p>
<pre class="r"><code>library("biomformat"); packageVersion("biomformat")</code></pre>
-<pre><code>## [1] '1.4.0'</code></pre>
+<pre><code>## [1] '1.6.0'</code></pre>
</div>
<div id="read-biom-format" class="section level1">
<h1><span class="header-section-number">1</span> Read BIOM format</h1>
@@ -199,11 +266,11 @@ x1</code></pre>
<h3><span class="header-section-number">2.0.4</span> Plots</h3>
<p>The data really is accessible to other R functions.</p>
<pre class="r"><code>plot(biom_data(x4))</code></pre>
-<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAA2AAAAKgCAMAAADK0+6WAAADAFBMVEUAAAABAQECAgIDAwMEBAQFBQUGBgYHBwcICAgJCQkKCgoLCwsMDAwNDQ0ODg4PDw8QEBARERESEhITExMUFBQVFRUWFhYXFxcYGBgZGRkaGhobGxscHBwdHR0eHh4fHx8gICAhISEiIiIjIyMkJCQlJSUmJiYnJycoKCgpKSkqKiorKyssLCwtLS0uLi4vLy8wMDAxMTEyMjIzMzM0NDQ1NTU2NjY3Nzc4ODg5OTk6Ojo7Ozs8PDw9PT0+Pj4/Pz9AQEBBQUFCQkJDQ0NERERFRUVGRkZHR0dISEhJSUlKSkpLS0tMTExNTU1OTk5PT09QUFBRUVFSUlJTU1NUVFRVVVVWVlZXV1dYWFhZWVlaWlpbW1tcXFxdXV1eXl5fX19gYGBhYWFiYmJjY2NkZ [...]
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<pre class="r"><code>boxplot(as(biom_data(x4), "vector"))</code></pre>
-<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAA2AAAAKgCAMAAADK0+6WAAACslBMVEUAAAABAQECAgIDAwMEBAQFBQUGBgYHBwcICAgJCQkKCgoLCwsMDAwNDQ0ODg4PDw8QEBARERESEhITExMUFBQVFRUWFhYXFxcYGBgZGRkaGhobGxscHBwdHR0eHh4fHx8gICAiIiIjIyMkJCQlJSUmJiYnJycoKCgpKSkqKiorKyssLCwtLS0uLi4vLy8wMDAzMzM1NTU2NjY3Nzc4ODg6Ojo7Ozs8PDw9PT0/Pz9AQEBBQUFCQkJDQ0NERERGRkZHR0dJSUlKSkpMTExNTU1OTk5PT09QUFBRUVFSUlJTU1NUVFRVVVVWVlZXV1dYWFhZWVlaWlpbW1tcXFxeXl5fX19gYGBhYWFiYmJjY2NkZGRlZWVmZmZpaWlqampra2tsbGxtbW1ubm5wcHBxc [...]
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<pre class="r"><code>heatmap(as(biom_data(x4), "matrix"))</code></pre>
-<p><img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAA2AAAAKgCAIAAAByb4nzAAAACXBIWXMAAA7DAAAOwwHHb6hkAAAgAElEQVR4nOzdfVyV9f348c8lBw5yuBFRuRFNzHsRFOdIUxBNxaVlW0siN1rgmummFjOU5thUygc5pGVCW2tWm5pg25QcOrENRIsGePcVExBTE44yQW7i7nh+f5zfGB+0w+H2Ank9/9gjr3N9rut9bNmr65zrQjEajQIAAAD4r35qDwAAAICehUAEAACAhEAEAACARKP2AABaevHFF41Go1arVXuQHqGxsfHixYvjx49Xe5Ce4saNGwsXLnzyySfVHgTA/YxABHqcjz/+eO7cuW5ubmoP0iM0NjY6OTk5OzurPUhPkZ2dnZGRQSAC6FIEItDjODs7/+AHP3jooYfUHgQ9UWVlZf/+/dWeAsB9ju8gAgAAQEIgAgAAQEIgA [...]
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</div>
</div>
<div id="write-biom-format" class="section level1">
@@ -223,12 +290,41 @@ system(paste0("FC ", rich_sparse_file, outfile))</code></pre>
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</script>
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