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Manually fix formatting problem in canine-aldex.html
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Formatting problem in the html was caused by lack of new line after the
call to `kable()` in the Rmd file. I added the new line to the Rmd, but
fixed the html formatting manually to avoid having to re-run the
analysis.
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mikemc committed Feb 28, 2020
1 parent 8e61beb commit ee1c13b
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Showing 2 changed files with 3 additions and 45 deletions.
3 changes: 2 additions & 1 deletion analysis/canine-aldex.Rmd
Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,8 @@ top_hits %>%
select(-Phylum) %>%
knitr::kable(digits = 3)
```
The top differentially abundant taxa according to ALDEx2 mainly have p-valuse <

The top differentially abundant taxa according to ALDEx2 mainly have p-values <
0.05 by the Fisher test, and in the expected direction. This observation is
consistent with the idea that ALDEx2 is mainly picking up presence/absence
patterns, which we explore visually below.
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45 changes: 1 addition & 44 deletions analysis/canine-aldex.html
Original file line number Diff line number Diff line change
Expand Up @@ -2443,52 +2443,9 @@ <h2>Aldex</h2>
<td align="right">0.371</td>
<td align="right">0.048</td>
</tr>
<tr class="odd">
<td align="left">The top d</td>
<td align="right">ifferenti</td>
<td align="right">ally abu</td>
<td align="right">ndant tax</td>
<td align="right">a accord</td>
<td align="right">ing to AL</td>
<td align="left">DEx2 mainly have p-valuse &lt;</td>
<td align="right"></td>
<td align="right"></td>
</tr>
<tr class="even">
<td align="left">0.05 by t</td>
<td align="right">he Fisher</td>
<td align="right">test, a</td>
<td align="right">nd in the</td>
<td align="right">expecte</td>
<td align="right">d directi</td>
<td align="left">on. This observation is</td>
<td align="right"></td>
<td align="right"></td>
</tr>
<tr class="odd">
<td align="left">consisten</td>
<td align="right">t with th</td>
<td align="right">e idea t</td>
<td align="right">hat ALDEx</td>
<td align="right">2 is mai</td>
<td align="right">nly picki</td>
<td align="left">ng up presence/absence</td>
<td align="right"></td>
<td align="right"></td>
</tr>
<tr class="even">
<td align="left">patterns,</td>
<td align="right">which we</td>
<td align="right">explore</td>
<td align="right">visually</td>
<td align="right">below.</td>
<td align="right"></td>
<td align="left"></td>
<td align="right"></td>
<td align="right"></td>
</tr>
</tbody>
</table>
<p>The top differentially abundant taxa according to ALDEx2 mainly have p-values &lt; 0.05 by the Fisher test, and in the expected direction. This observation is consistent with the idea that ALDEx2 is mainly picking up presence/absence patterns, which we explore visually below.</p>
<pre class="r"><code># Pick the top 4 positive and negative associations, plus ASV62
taxa &lt;- x.all %&gt;%
group_by(sign(effect)) %&gt;%
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