Merge pull request #596 from d3b-center/rokita/rerun-tables

rerun tables for manuscript

tables/01-output_tables.nb.html

@@ -2939,9 +2939,9 @@ <h1>Read files</h1>
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 <pre class="r"><code>histology_df &lt;- read_tsv(histology_file, guess_max =100000)</code></pre>
 <!-- rnb-source-end -->
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 <pre><code>Rows: 47895 Columns: 66
-── Column specification ───────────────────────────────────────────────────────────────────────────────────────────
+── Column specification ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 Delimiter: &quot;\t&quot;
 chr (45): 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...

tables/02-molecular_subtype_table.R

@@ -5,6 +5,7 @@ library(openxlsx)
 root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
 input_dir <- file.path(root_dir, "data")
 output_dir <- file.path(root_dir, "tables", "results")
+mb_dir <- file.path(root_dir, "analyses", "molecular-subtyping-MB", "results")
 
 ## read file
 hist <- read_tsv(file.path(input_dir, "histologies.tsv"))
@@ -40,8 +41,7 @@ hist_combined <- hist_combined %>%
  Patients = sum(hist_combined$Patients))
 
 ## MB subtype 
-## change the directory once the PR is merged ##
-MB_subtype <- read_tsv(file.path(output_dir, "mb_shh_molecular_subtypes.tsv"))
+MB_subtype <- read_tsv(file.path(mb_dir, "mb_shh_molecular_subtypes.tsv"))
 
 ## fianl table
 final_table <- list(histologies_summary = hist_combined, 

tables/03-software_version.html

@@ -1629,13 +1629,13 @@ <h4 class="date">2024-05-30</h4>
 
 
 <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>

tables/README.md

@@ -1,10 +1,21 @@
-## Table Generation - Histologies File with README
+## Manuscript table generation
 
 This module (`output_tables.Rmd`) creates tables and supplementary tables for the manuscript.
 
-Release: v14
+Release: v15
 
-Histologies table
+1. Histologies table
 - This table displays the histologies file from OpenPedCan in an excel format.
  - Sheet 1: README
- - Sheet 2: Histologies file
+ - Sheet 2: Histologies file
+
+2. Molecular Subtype table
+- This table displays the histologies file from OpenPedCan in an excel format.
+ - Sheet 1: Subtype totals by tumor/patient
+ - Sheet 2: MB SHH subtypes
+
+3. Software table
+- This table displays the histologies file from OpenPedCan in an excel format.
+ - Sheet 1: R packages
+ - Sheet 2: python libraries
+ - Sheet 3: CLI tools