From e87e60d3035a3e4226ccc30b011375acea7f5b51 Mon Sep 17 00:00:00 2001
From: TuomasBorman <TuomasBorman@users.noreply.github.com>
Date: Sat, 18 Jan 2025 21:27:19 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20microbio?=
 =?UTF-8?q?me/mia@26201a1c08cf96531741c79dbe6408bdfc9958b6=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pkgdown.yml                     |   2 +-
 reference/addLDA-1.png          | Bin 18775 -> 18818 bytes
 reference/addLDA.html           |  12 ++++++------
 reference/taxonomy-methods.html |  27 ++++++++++++++++++++++++++-
 4 files changed, 33 insertions(+), 8 deletions(-)

diff --git a/pkgdown.yml b/pkgdown.yml
index e36ca13a9..da4fe716c 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,4 +3,4 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   mia: mia.html
-last_built: 2025-01-18T20:52Z
+last_built: 2025-01-18T21:23Z
diff --git a/reference/addLDA-1.png b/reference/addLDA-1.png
index b8893a17ec014228f0a47419c5add5fe72b4c530..de53b1e1564903074732b5ebb89cc90b5c926483 100644
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diff --git a/reference/addLDA.html b/reference/addLDA.html
index ada1ee50d..ce3920488 100644
--- a/reference/addLDA.html
+++ b/reference/addLDA.html
@@ -137,12 +137,12 @@ <h2>Examples</h2>
 <span class="r-in"><span><span class="va">loadings</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/attr.html" class="external-link">attr</a></span><span class="op">(</span><span class="fu">reducedDim</span><span class="op">(</span><span class="va">tse</span>, <span class="st">"LDA"</span><span class="op">)</span>, <span class="st">"loadings"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">loadings</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                            1            2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> AD3             0.0014369272 1.558145e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Acidobacteria   0.0533073361 2.271935e-05</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Actinobacteria  0.1650020225 2.926029e-02</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Armatimonadetes 0.0007549467 1.372823e-05</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> BRC1            0.0001038350 1.297049e-07</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Bacteroidetes   0.0823659390 2.924730e-01</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> AD3             1.715098e-07 0.0014954904</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Acidobacteria   2.731971e-05 0.0554732446</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Actinobacteria  3.080708e-02 0.1682332078</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Armatimonadetes 1.175229e-05 0.0007881141</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> BRC1            1.211369e-07 0.0001080765</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Bacteroidetes   2.904886e-01 0.0767541128</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Estimate models with number of topics from 2 to 10</span></span></span>
 <span class="r-in"><span><span class="va">tse</span> <span class="op">&lt;-</span> <span class="fu">addLDA</span><span class="op">(</span><span class="va">tse</span>, k <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">2</span>, <span class="fl">3</span>, <span class="fl">4</span>, <span class="fl">5</span>, <span class="fl">6</span>, <span class="fl">7</span>, <span class="fl">8</span>, <span class="fl">9</span>, <span class="fl">10</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"LDA_10"</span><span class="op">)</span></span></span>
diff --git a/reference/taxonomy-methods.html b/reference/taxonomy-methods.html
index 20e8405ca..e111d84ab 100644
--- a/reference/taxonomy-methods.html
+++ b/reference/taxonomy-methods.html
@@ -293,6 +293,31 @@ <h2>Examples</h2>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [15] "Family:Cenarchaeaceae"            "Family:Cenarchaeaceae_1"         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [17] "Family:Cenarchaeaceae_2"          "Family:Cenarchaeaceae_3"         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [19] "Family:Cenarchaeaceae_4"          "Family:Cenarchaeaceae_5"         </span>
+<span class="r-in"><span><span class="co"># Taxonomy labels represent the lowest taxonomy name that identifies each</span></span></span>
+<span class="r-in"><span><span class="co"># taxa. For instance, they can represent OTUs which does no necessarily</span></span></span>
+<span class="r-in"><span><span class="co"># tell much. In this case, you might want to get the labels with higher</span></span></span>
+<span class="r-in"><span><span class="co"># taxonomy rank</span></span></span>
+<span class="r-in"><span><span class="fu">getTaxonomyLabels</span><span class="op">(</span><span class="va">GlobalPatterns</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">20</span>,<span class="op">]</span>, lowest.rank <span class="op">=</span> <span class="st">"Class"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "Thermoprotei"                                                               </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2] "Thermoprotei_1"                                                             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3] "Thermoprotei_Sulfolobales_Sulfolobaceae_Sulfolobus_Sulfolobusacidocaldarius"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4] "Sd-NA"                                                                      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "Sd-NA_1"                                                                    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6] "Sd-NA_2"                                                                    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] "Sd-NA_NRP-J"                                                                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] "Sd-NA_NRP-J_1"                                                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "Sd-NA_NRP-J_2"                                                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] "Sd-NA_NRP-J_3"                                                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] "Sd-NA_NRP-J_4"                                                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [12] "Thaumarchaeota_Cenarchaeales_SAGMA-X"                                       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "Thaumarchaeota_Cenarchaeales_SAGMA-X_1"                                     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [14] "Thaumarchaeota_Cenarchaeales_SAGMA-X_2"                                     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [15] "Thaumarchaeota_Cenarchaeales_Cenarchaeaceae"                                </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "Thaumarchaeota_Cenarchaeales_Cenarchaeaceae_1"                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "Thaumarchaeota_Cenarchaeales_Cenarchaeaceae_2"                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [18] "Thaumarchaeota_Cenarchaeales_Cenarchaeaceae_3"                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] "Thaumarchaeota_Cenarchaeales_Cenarchaeaceae_4"                              </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [20] "Thaumarchaeota_Cenarchaeales_Cenarchaeaceae_5"                              </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># mapTaxonomy</span></span></span>
 <span class="r-in"><span><span class="co">## returns the unique taxonomic information</span></span></span>
@@ -345,7 +370,7 @@ <h2>Examples</h2>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">tse</span><span class="op">)</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">&lt;-</span> <span class="st">"TAXA1"</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">setTaxonomyRanks</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/pkg/SummarizedExperiment/man/SummarizedExperiment-class.html" class="external-link">rowData</a></span><span class="op">(</span><span class="va">tse</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="co"># Taxonomy ranks set to: taxa1 phylum class order family genus species </span></span></span>
+<span class="r-in"><span><span class="co"># Taxonomy ranks set to: taxa1 phylum class order family genus species</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># getTaxonomyRanks is to get/check if the taxonomic ranks is set to "TAXA1"</span></span></span>
 <span class="r-in"><span><span class="fu">getTaxonomyRanks</span><span class="op">(</span><span class="op">)</span></span></span>