Merge pull request #54 from d3b-center/rjcorb/49-demo-clin-stats

Add module to assess demographic and clinical summary stats by predicted ancestry
d3b-center · Feb 29, 2024 · a6ae544 · a6ae544
2 parents 5683878 + f842b24
commit a6ae544
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Showing 11 changed files with 4,042 additions and 48 deletions.
diff --git a/analyses/add-histologies/01-add_histologies.html b/analyses/add-histologies/01-add_histologies.html
@@ -430,13 +430,13 @@ <h4 class="date">2023</h4>
 <p>Load libraries and set directories</p>
 <pre class="r"><code>library(data.table)
 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     1.1.1     ✔ readr     2.1.4
 ## ✔ forcats   1.0.0     ✔ stringr   1.5.0
 ## ✔ ggplot2   3.4.2     ✔ tibble    3.2.1
 ## ✔ lubridate 1.9.2     ✔ tidyr     1.3.0
 ## ✔ purrr     1.0.1     
-## ── Conflicts ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
+## ── Conflicts ────────────────────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
 ## ✖ dplyr::between()     masks data.table::between()
 ## ✖ dplyr::filter()      masks stats::filter()
 ## ✖ dplyr::first()       masks data.table::first()
@@ -477,7 +477,7 @@ <h4 class="date">2023</h4>
 <h2>Read in somalier results and histologies files</h2>
 <pre class="r"><code>ancestry &lt;- read_tsv(ancestry_file)</code></pre>
 <pre><code>## Rows: 1513 Columns: 13
-## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: &quot;\t&quot;
 ## chr  (2): Kids_First_Biospecimen_ID, predicted_ancestry
 ## dbl (10): EAS_prob, AFR_prob, AMR_prob, SAS_prob, EUR_prob, PC1, PC2, PC3, P...
@@ -487,7 +487,7 @@ <h2>Read in somalier results and histologies files</h2>
 ## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.</code></pre>
 <pre class="r"><code>hist &lt;- read_tsv(hist_file, guess_max = 1000000)</code></pre>
 <pre><code>## Rows: 47633 Columns: 58
-## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: &quot;\t&quot;
 ## chr (41): Kids_First_Participant_ID, Kids_First_Biospecimen_ID, sample_id, a...
 ## dbl (17): cell_line_passage, OS_days, EFS_days, age_at_diagnosis_days, age_a...
@@ -511,7 +511,7 @@ <h2>Add data columns from histology file</h2>
 # read in plot_mapping file to add plot group to results
 plot_mapping &lt;- read_tsv(plot_mapping_file)</code></pre>
 <pre><code>## Rows: 79 Columns: 9
-## ── Column specification ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
+## ── Column specification ────────────────────────────────────────────────────────────────────────────────────────────────────
 ## Delimiter: &quot;\t&quot;
 ## chr (8): broad_histology, cancer_group, broad_histology_display, plot_group,...
 ## dbl (1): broad_histology_order