changed look, warnings and code echo off

webpage_contents/_quarto.yml

@@ -39,6 +39,11 @@ website:
     
 format: 
     html:
-       toc: true       
-       toc-depth: 4      
-       embed-resources: true
+      toc: true       
+      toc-depth: 4      
+      embed-resources: true
+      grid: 
+        body-width: 1500px
+
+echo: false
+warning: false

webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd

@@ -13,7 +13,7 @@ author:
     orcid: 0000-0003-2665-0995
     affiliations:
       - name: The Interface Group, Institute of Physiology, University of Zurich
-code-fold: true
+
 ---
 ## Setup
 [test_link](https://gitlab.uzh.ch/)
@@ -47,9 +47,6 @@ Three dimensional rendering of CSF spaces enclosed in the mouse skull: Infusion
 ## Links to protocol pages
 
 ```{r}
-# | warning: false 
-
-
 library(dplyr)
 
 # This code chunk gathers the rows from tables specified in the inputs
@@ -72,23 +69,24 @@ DT::datatable(paths, options = list(dom = 't'), escape = FALSE, rownames = FALSE
 ## Sample information
 
 ```{r}
-# | warning: false 
-
 library(dplyr)
+
 # Take the relevant rows from the tables specified in inputs
 data_used <- list()
 for (i in 1:nrow(inputs)){ 
   row_filepath <- file.path(here::here(), 'experiments',inputs$Data_type[i], inputs$Facility_name_YYYY_month[i], "metadata_tables", inputs$Metadata_file[i]) 
   data_used[[i]] <- read.csv(row_filepath) %>% filter(Subject_ID == inputs$Subject_ID[i]) # read table and filter subject
+  
+  # Add additional columns from 'input_mice' tables into the mouse_list table that will be displayed
+  data_used[[i]]$Subject_pubID <- inputs$Subject_pubID[i]  
+  data_used[[i]]$Correction_factor <- inputs$Correction_factor[i] # Add additional input column
 }
 
-# Gather list elements in a table 
+# Gather all rows elements in a table 
 data_used <- do.call(rbind,data_used) 
-data_used$Subject_pubID <- inputs$Subject_pubID # Add additional input column 
-data_used$correction_factor <- inputs$Correction_factor # Add additional input column
-data_used <- relocate(data_used, Correction_factor, .before = 7)
 
-# add the subject index for publication as first variable
+# Change position of some columns
+data_used <- relocate(data_used, Correction_factor, .before = 7)
 data_used <- relocate(data_used, Subject_pubID, .before = 1)
 
 #Display  table