comment error lines publication page

webpage_contents/publications/20240901_Marta_GironaAlarcon/Publication_page.qmd

+---
+title: 'In vivo Imaging of Central Nervous System Fluid Spaces using Synchrotron Radiation Micro-Computed Tomography'
+date: '2024-09-01'
+First author: 'Marta Girona Alarcón'
+Last author: 'Vartan Kurtcuoglu'
+author: 
+  - name: 'Marta Girona Alarcón (first author)'
+    orcid: 0009-0006-2111-2716     
+    affiliations:
+      - name: The Interface Group, Institute of Physiology, University of Zurich
+
+  - name: 'Vartan Kurtcuoglu (last author)'
+    orcid: 0000-0003-2665-0995
+    affiliations:
+      - name: The Interface Group, Institute of Physiology, University of Zurich
+code-fold: true
+---
+# Setup images
+
+# Supplemental Results
+## Experiment 2: CSF spaces segmentation
+- add rendering of in vivo CSF spaces (link to Zenodo)
+
+## Experiment 4: Contrast agent dynamics during lateral ventricle influsion
+- add movie (link to Zenodo)
+
+## Experiment 6: Cardiac-gated 3D imaging
+- add movie (link to Zenodo)
+
+## Experiment 7: Non-periodic ChP movement within the lateral ventricle
+- add movie (link to Zenodo)
+
+## Discussion: CSF flow back to the infusion cannula
+- add projections movie (link to Zenodo)
+
+
+<!-- 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')
+
+``` -->
+