Merge pull request #602 from d3b-center/rjcorb/update-mb-shh-abridged…

…-output update MB SHH abridged output
d3b-center · Sep 25, 2024 · 73bf9cd · 73bf9cd
2 parents 945dfab + 13b1d13
commit 73bf9cd
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diff --git a/analyses/molecular-subtyping-MB/00-mb-select-pathology-dx.html b/analyses/molecular-subtyping-MB/00-mb-select-pathology-dx.html
@@ -1676,13 +1676,13 @@ <h2>Background</h2>
 <div id="set-up" class="section level2">
 <h2>Set up</h2>
 <pre class="r"><code>library(tidyverse)</code></pre>
-<pre><code>## ── Attaching core tidyverse packages ───────────────────────────────────────────────────────── tidyverse 2.0.0 ──
+<pre><code>## ── Attaching core tidyverse packages ────────────────────────────────────────────────────────────────────── tidyverse 2.0.0 ──
 ## ✔ dplyr     1.1.4     ✔ readr     2.1.5
 ## ✔ forcats   1.0.0     ✔ stringr   1.5.1
 ## ✔ ggplot2   3.5.1     ✔ tibble    3.2.1
 ## ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
 ## ✔ purrr     1.0.2     
-## ── Conflicts ─────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+## ── Conflicts ──────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 ## ✖ dplyr::filter() masks stats::filter()
 ## ✖ dplyr::lag()    masks stats::lag()
 ## ℹ Use the conflicted package (&lt;http://conflicted.r-lib.org/&gt;) to force all conflicts to become errors</code></pre>
@@ -1699,7 +1699,7 @@ <h2>Set up</h2>
 <h2>Read in data</h2>
 <pre class="r"><code>histologies_df &lt;- read_tsv(histologies_file)</code></pre>
 <pre><code>## Rows: 47895 Columns: 64
-## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: &quot;\t&quot;
 ## chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
 ## dbl (21): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...

diff --git a/analyses/molecular-subtyping-MB/05-subtype-mb-shh.R b/analyses/molecular-subtyping-MB/05-subtype-mb-shh.R
@@ -377,7 +377,7 @@ final_subtypes <- mb_subtypes %>%
 
 final_subtypes %>%
   select("Kids_First_Participant_ID", "Kids_First_Biospecimen_ID", "match_id", "sample_id", 
-         "molecular_subtype", "molecular_subtype_methyl", "SHH_subtype", "tp53_status",
+         "molecular_subtype", "molecular_subtype_methyl", "tp53_status",
          classification_source) %>%
   write_tsv(file.path(results_dir, "mb_shh_molecular_subtypes.tsv"))
 

diff --git a/analyses/molecular-subtyping-MB/06-mb-shh-umap.html b/analyses/molecular-subtyping-MB/06-mb-shh-umap.html
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb.pdf
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb_group34.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb_group34.pdf
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb_shh.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb_shh.pdf
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb_shh_cn_status.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb_shh_cn_status.pdf
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb_shh_methylation_subtype.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb_shh_methylation_subtype.pdf
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb_shh_tp53_status.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb_shh_tp53_status.pdf
diff --git a/analyses/molecular-subtyping-MB/plot/umap_mb_wnt.pdf b/analyses/molecular-subtyping-MB/plot/umap_mb_wnt.pdf
diff --git a/analyses/molecular-subtyping-MB/results/mb_shh_molecular_subtypes.tsv b/analyses/molecular-subtyping-MB/results/mb_shh_molecular_subtypes.tsv