From 7322a3c1e2ee561701eddacb2da79745915ab761 Mon Sep 17 00:00:00 2001
From: Willy Kuo <willy.kuo@physiol.uzh.ch>
Date: Wed, 26 Jun 2024 15:06:09 +0200
Subject: [PATCH] Added instructions to the Publication Page
---
.../Publication_page.qmd | 20 +++-
.../Publication_page.qmd.backup | 97 +++++++++++++++++++
2 files changed, 115 insertions(+), 2 deletions(-)
create mode 100644 webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd.backup
diff --git a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
index 3ffafc6..52c85e2 100644
--- a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
+++ b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd
@@ -16,7 +16,23 @@ author:
code-fold: true
---
-
+<!-- Delete the instructions section after copying this template !! -->
+
+# Instructions for editing
+This Publication Page is meant to only contain information specific to the publication it's describing. Supplemental Methods that may be reused for another publication are supposed to go to the respective Experiment Page.
+
+Possible examples for non-reuseable information that could go on this page:
+
+- Supplemental results
+- Supplemental figures
+- Download links to supplemental videos, e.g. on Zenodo
+- Data processing methods that are specific to the publication's research question
+
+Programming code for pulling the information on samples or individual scans is at the bottom of the page. Editing the samples required happens not here, but in the Input_mice.csv file. Do not edit the code below the demarcated line, to avoid breaking the functionality.
+
+
+
+
# Supplemental Results
Here you can enter information about your results in text (with markdown format)
@@ -54,7 +70,7 @@ DT::datatable(paths, options = list(dom = 't'), escape = FALSE, rownames = FALSE
```
-## Mice information
+## Sample information
```{r}
# | warning: false
diff --git a/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd.backup b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd.backup
new file mode 100644
index 0000000..b927409
--- /dev/null
+++ b/webpage_contents/templates/templates_for_publications/YYYYMMDD_Firstname_LastName/Publication_page.qmd.backup
@@ -0,0 +1,97 @@
+---
+title: 'Publication Title'
+date: '0000-01-30'
+First author: 'First Author Fullname'
+Last author: 'Last Author Fullname'
+author:
+ - name: 'First Author Fullname'
+ orcid: 1234-1234-1234-1234
+ affiliations:
+ - name: Group name, Institute name, University name
+
+ - name: 'Second Author Fullname'
+ orcid: 1234-1234-1234-1234
+ affiliations:
+ - name: Group name, Institute name, University name
+code-fold: true
+---
+
+<!-- Delete the instructions section after copying this template !! -->
+
+# Instructions for editing
+This Publication Page is meant to only contain information specific to the publication it's describing. Supplemental Methods that may be reused for another publication are supposed to go to the respective Experiment Page.
+
+Possible examples for non-reuseable information that could go on this page:
+
+- Supplemental results
+- Supplemental figures
+- Download links to supplemental videos, e.g. on Zenodo
+- Data processing methods that are specific to the publication's research question
+
+Programming code for pulling the information on samples or individual scans is at the bottom of the page. Editing the samples required happens not here, but in the Input_mice.csv file. Do not edit the code
+
+
+
+
+# Supplemental Results
+Here you can enter information about your results in text (with markdown format)
+
+
+
+
+
+
+
+
+<!-- Do not edit below this line !! -->
+
+## Links to protocol pages
+
+```{r}
+# | warning: false
+
+
+library(dplyr)
+
+# This code chunk gathers the rows from tables specified in the inputs
+inputs <- read.csv(file = 'input_mice.csv')
+
+# Use data type and facility information to find the path to the relevant protocols
+folders <- unique(cbind(inputs$Data_type,inputs$Facility_name_mon_YYYY)) # find table's unique variations of experiment type and facility
+paths <- as.data.frame(file.path(apply(folders, 1, paste, collapse = .Platform$file.sep), 'protocols')) #put together the paths
+colnames(paths) <- 'Protocols'
+
+# Add HTML code so that it becomes a clickable link
+paths$Protocols <- paste0('<a href=\'',paths$Protocols,'\' target=\'_blank\'>', paths$Protocols,'</a>')
+file.path(here::here(), apply(folders, 1, paste, collapse = .Platform$file.sep), 'protocols')
+
+# Render table
+DT::datatable(paths, options = list(dom = 't'), escape = FALSE, rownames = FALSE, )
+
+```
+
+## Sample information
+
+```{r}
+# | warning: false
+
+library(dplyr)
+# Take the relevant rows from the tables specified in inputs
+data_used <- list()
+for (i in 1:nrow(inputs)){
+ row_filepath <- file.path(here::here(), 'experiments',inputs$Data_type[i], inputs$Facility_name_mon_YYYY[i], inputs$Metadata_file[i])
+ data_used[[i]] <- read.csv(row_filepath) %>% filter(SubjectID == inputs$SubjectID[i]) # read table and filter subject
+}
+
+# Gather list elements in a table
+data_used <- do.call(rbind,data_used)
+data_used$Subject_pubID <- inputs$Subject_pubID # Add additional input column
+
+# add the subject index for publication as first variable
+data_used <- relocate(data_used, Subject_pubID, .before = 1)
+
+#Display table
+DT::datatable(data_used, filter = 'top')
+
+```
+
--
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