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Add sample numbers for scatterplots
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sjessa committed Oct 18, 2022
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15 changes: 15 additions & 0 deletions code/02-bulk_comparisons.Rmd
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Expand Up @@ -242,6 +242,21 @@ save(data_chip_stats, file = glue("{out}/data_chip_stats.Rda"))
```


Count samples:

```{r count_samples}
data_chip_tidy %>%
left_join(meta %>% distinct(ID_paper, Group), by = "ID_paper") %>%
distinct(ID_paper, Group, Mark) %>%
group_by(Group, Mark) %>%
count() %>%
filter(Group %in% c("HGG-H3.1/2K27M-Pons",
"HGG-H3.3K27M-Pons",
"HGG-H3.3K27M-Thal."))
```

## Scatterplot for H3.1 vs H3.3 pons

Here, we'll combine the DGE data with each of different source of ChIP-seq analysis,
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32 changes: 20 additions & 12 deletions code/02-bulk_comparisons.html
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Expand Up @@ -190,7 +190,7 @@ <h4 class="author">Selin Jessa [<script type="text/javascript">
document.write('<a h'+'ref'+'="ma'+'ilto'+':'+e+'" clas'+'s="em' + 'ail">'+e+'<\/'+'a'+'>');
// -->
</script><noscript>selin.jessa at mail dot mcgill dot ca</noscript>]</h4>
<h4 class="date">08 September, 2022</h4>
<h4 class="date">18 October, 2022</h4>

</div>

Expand Down Expand Up @@ -400,6 +400,20 @@ <h2><span class="header-section-number">6.1</span> Load data</h2>
pivot_wider(names_from = statistic, values_from = value)

save(data_chip_stats, file = glue(&quot;{out}/data_chip_stats.Rda&quot;))</code></pre>
<p>Count samples:</p>
<pre class="r"><code>data_chip_tidy %&gt;%
left_join(meta %&gt;% distinct(ID_paper, Group), by = &quot;ID_paper&quot;) %&gt;%
distinct(ID_paper, Group, Mark) %&gt;%
group_by(Group, Mark) %&gt;%
count() %&gt;%
filter(Group %in% c(&quot;HGG-H3.1/2K27M-Pons&quot;,
&quot;HGG-H3.3K27M-Pons&quot;,
&quot;HGG-H3.3K27M-Thal.&quot;))</code></pre>
<div data-pagedtable="false">
<script data-pagedtable-source type="application/json">
{"columns":[{"label":["Group"],"name":[1],"type":["chr"],"align":["left"]},{"label":["Mark"],"name":[2],"type":["chr"],"align":["left"]},{"label":["n"],"name":[3],"type":["int"],"align":["right"]}],"data":[{"1":"HGG-H3.1/2K27M-Pons","2":"H3K27ac","3":"14"},{"1":"HGG-H3.1/2K27M-Pons","2":"H3K27me3","3":"3"},{"1":"HGG-H3.3K27M-Pons","2":"H3K27ac","3":"16"},{"1":"HGG-H3.3K27M-Pons","2":"H3K27me3","3":"6"},{"1":"HGG-H3.3K27M-Thal.","2":"H3K27ac","3":"5"},{"1":"HGG-H3.3K27M-Thal.","2":"H3K27me3","3":"4"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
</script>
</div>
</div>
<div id="scatterplot-for-h3.1-vs-h3.3-pons" class="section level2">
<h2><span class="header-section-number">6.2</span> Scatterplot for H3.1 vs H3.3 pons</h2>
Expand Down Expand Up @@ -496,11 +510,11 @@ <h2><span class="header-section-number">6.3</span> Scatterplot for H3.3 pons vs
<div id="reproducibility" class="section level1">
<h1><span class="header-section-number">7</span> Reproducibility</h1>
<p>This document was last rendered on:</p>
<pre><code>## 2022-09-08 15:08:33</code></pre>
<pre><code>## 2022-10-18 14:17:13</code></pre>
<p>The git repository and last commit:</p>
<pre><code>## Local: master /lustre06/project/6004736/sjessa/from_narval/HGG-oncohistones/public
## Remote: master @ origin (git@github.com:fungenomics/HGG-oncohistones.git)
## Head: [4101e76] 2022-09-08: Update README.md</code></pre>
## Head: [8082a4d] 2022-10-18: Merge branch 'master' of github.com:fungenomics/HGG-oncohistones</code></pre>
<p>The random seed was set with <code>set.seed(100)</code></p>
<p>The R session info: <details></p>
<pre><code>## Error in get(genname, envir = envir) : object 'testthat_print' not found</code></pre>
Expand All @@ -514,7 +528,7 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## collate en_CA.UTF-8
## ctype en_CA.UTF-8
## tz EST5EDT
## date 2022-09-08
## date 2022-10-18
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date lib
Expand All @@ -539,7 +553,6 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## P ellipsis 0.3.2 2021-04-29 [?]
## P evaluate 0.14 2019-05-28 [?]
## P fansi 0.4.2 2021-01-15 [?]
## P farver 2.1.0 2021-02-28 [?]
## P fastmap 1.1.0 2021-01-25 [?]
## P feather * 0.3.5 2019-09-15 [?]
## P fitdistrplus 1.1-3 2020-12-05 [?]
Expand All @@ -557,7 +570,6 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## P gridExtra 2.3 2017-09-09 [?]
## P gtable 0.3.0 2019-03-25 [?]
## P here * 0.1 2017-05-28 [?]
## P highr 0.9 2021-04-16 [?]
## P hms 1.0.0 2021-01-13 [?]
## P htmltools 0.5.1.1 2021-01-22 [?]
## P htmlwidgets 1.5.3 2020-12-10 [?]
Expand All @@ -571,7 +583,6 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## P jsonlite 1.7.2 2020-12-09 [?]
## P KernSmooth 2.23-15 2015-06-29 [?]
## P knitr 1.33 2021-04-24 [?]
## P labeling 0.4.2 2020-10-20 [?]
## P later 1.0.0 2019-10-04 [?]
## P lattice 0.20-44 2021-05-02 [?]
## P lazyeval 0.2.2 2019-03-15 [?]
Expand Down Expand Up @@ -698,8 +709,6 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## Github (fungenomics/icytobox@730e8b8)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
Expand Down Expand Up @@ -772,7 +781,6 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## Github (rmflight/testrmd@0735c20)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
Expand All @@ -791,14 +799,14 @@ <h1><span class="header-section-number">7</span> Reproducibility</h1>
## CRAN (R 3.6.1)
##
## [1] /lustre06/project/6004736/sjessa/from_narval/HGG-oncohistones/public/renv/library/R-3.6/x86_64-pc-linux-gnu
## [2] /tmp/RtmpPXZ49F/renv-system-library
## [2] /tmp/Rtmp7TyGB4/renv-system-library
##
## P ── Loaded and on-disk path mismatch.</code></pre>
<p></details></p>
<p>The resources requested when this document was last rendered:</p>
<pre><code>## #SBATCH --time=01:00:00
## #SBATCH --cpus-per-task=1
## #SBATCH --mem=10G</code></pre>
## #SBATCH --mem=20G</code></pre>
<hr />
<!-- END OF END MATTER -->
</div>
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39 changes: 27 additions & 12 deletions code/02-bulk_comparisons.md
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@@ -1,7 +1,7 @@
---
title: "02 - Bulk RNAseq/ChIPseq comparisons"
author: "Selin Jessa [[selin.jessa@mail.mcgill.ca](mailto:selin.jessa@mail.mcgill.ca)]"
date: "08 September, 2022"
date: "18 October, 2022"
params:
resources: "NOT SPECIFIED"
output:
Expand Down Expand Up @@ -410,6 +410,27 @@ save(data_chip_stats, file = glue("{out}/data_chip_stats.Rda"))



Count samples:



```r
data_chip_tidy %>%
left_join(meta %>% distinct(ID_paper, Group), by = "ID_paper") %>%
distinct(ID_paper, Group, Mark) %>%
group_by(Group, Mark) %>%
count() %>%
filter(Group %in% c("HGG-H3.1/2K27M-Pons",
"HGG-H3.3K27M-Pons",
"HGG-H3.3K27M-Thal."))
```

<div data-pagedtable="false">
<script data-pagedtable-source type="application/json">
{"columns":[{"label":["Group"],"name":[1],"type":["chr"],"align":["left"]},{"label":["Mark"],"name":[2],"type":["chr"],"align":["left"]},{"label":["n"],"name":[3],"type":["int"],"align":["right"]}],"data":[{"1":"HGG-H3.1/2K27M-Pons","2":"H3K27ac","3":"14"},{"1":"HGG-H3.1/2K27M-Pons","2":"H3K27me3","3":"3"},{"1":"HGG-H3.3K27M-Pons","2":"H3K27ac","3":"16"},{"1":"HGG-H3.3K27M-Pons","2":"H3K27me3","3":"6"},{"1":"HGG-H3.3K27M-Thal.","2":"H3K27ac","3":"5"},{"1":"HGG-H3.3K27M-Thal.","2":"H3K27me3","3":"4"}],"options":{"columns":{"min":{},"max":[10]},"rows":{"min":[10],"max":[10]},"pages":{}}}
</script>
</div>

## Scatterplot for H3.1 vs H3.3 pons

Here, we'll combine the DGE data with each of different source of ChIP-seq analysis,
Expand Down Expand Up @@ -586,7 +607,7 @@ This document was last rendered on:


```
## 2022-09-08 15:08:33
## 2022-10-18 14:17:13
```


Expand All @@ -598,7 +619,7 @@ The git repository and last commit:
```
## Local: master /lustre06/project/6004736/sjessa/from_narval/HGG-oncohistones/public
## Remote: master @ origin (git@github.com:fungenomics/HGG-oncohistones.git)
## Head: [4101e76] 2022-09-08: Update README.md
## Head: [8082a4d] 2022-10-18: Merge branch 'master' of github.com:fungenomics/HGG-oncohistones
```


Expand Down Expand Up @@ -627,7 +648,7 @@ The R session info:
## collate en_CA.UTF-8
## ctype en_CA.UTF-8
## tz EST5EDT
## date 2022-09-08
## date 2022-10-18
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date lib
Expand All @@ -652,7 +673,6 @@ The R session info:
## P ellipsis 0.3.2 2021-04-29 [?]
## P evaluate 0.14 2019-05-28 [?]
## P fansi 0.4.2 2021-01-15 [?]
## P farver 2.1.0 2021-02-28 [?]
## P fastmap 1.1.0 2021-01-25 [?]
## P feather * 0.3.5 2019-09-15 [?]
## P fitdistrplus 1.1-3 2020-12-05 [?]
Expand All @@ -670,7 +690,6 @@ The R session info:
## P gridExtra 2.3 2017-09-09 [?]
## P gtable 0.3.0 2019-03-25 [?]
## P here * 0.1 2017-05-28 [?]
## P highr 0.9 2021-04-16 [?]
## P hms 1.0.0 2021-01-13 [?]
## P htmltools 0.5.1.1 2021-01-22 [?]
## P htmlwidgets 1.5.3 2020-12-10 [?]
Expand All @@ -684,7 +703,6 @@ The R session info:
## P jsonlite 1.7.2 2020-12-09 [?]
## P KernSmooth 2.23-15 2015-06-29 [?]
## P knitr 1.33 2021-04-24 [?]
## P labeling 0.4.2 2020-10-20 [?]
## P later 1.0.0 2019-10-04 [?]
## P lattice 0.20-44 2021-05-02 [?]
## P lazyeval 0.2.2 2019-03-15 [?]
Expand Down Expand Up @@ -811,8 +829,6 @@ The R session info:
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## Github (fungenomics/icytobox@730e8b8)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
Expand Down Expand Up @@ -885,7 +901,6 @@ The R session info:
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
## Github (rmflight/testrmd@0735c20)
## CRAN (R 3.6.1)
## CRAN (R 3.6.1)
Expand All @@ -904,7 +919,7 @@ The R session info:
## CRAN (R 3.6.1)
##
## [1] /lustre06/project/6004736/sjessa/from_narval/HGG-oncohistones/public/renv/library/R-3.6/x86_64-pc-linux-gnu
## [2] /tmp/RtmpPXZ49F/renv-system-library
## [2] /tmp/Rtmp7TyGB4/renv-system-library
##
## P ── Loaded and on-disk path mismatch.
```
Expand All @@ -920,7 +935,7 @@ The resources requested when this document was last rendered:
```
## #SBATCH --time=01:00:00
## #SBATCH --cpus-per-task=1
## #SBATCH --mem=10G
## #SBATCH --mem=20G
```


Expand Down

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