![](\"resources/images/Documentation2.png\")
![](\"resources/images/Publication2.png\")
;General", "Cancer Genome Collaboratory:![](\"resources/images/Hyperlink2.png\")
;General"))
+
+fulltab <- rows_delete(fulltab, duplicatesToRemove, by="PlatformCategory") %>%
+ select(-c(PlatformCategory))
+
```
```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
@@ -78,5 +80,6 @@ ITCR_ALL <- fulltab %>%
```
```{r,echo=FALSE,message=FALSE, warning=FALSE}
+#Display the whole table
ITCR_ALL
```
diff --git a/alldataFilesEditor.Rmd b/alldataFilesEditor.Rmd
deleted file mode 100644
index da4656a..0000000
--- a/alldataFilesEditor.Rmd
+++ /dev/null
@@ -1,87 +0,0 @@
----
-title: "**Data Files Editor**"
-output: html_document
----
-
-### **Overview**
-
-This file is used to make edits to the data files.
-
-```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-#Load DT, dplyr
-library(DT)
-#library(dplyr)
-library(here)
-library(tidyverse)
-library(magrittr)
-#library(RCurl)
-```
-
-## Resource table editor
-```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-# Load file for General Table
-#generalData <- read_csv(file = here::here("ictr_table_general.csv"))
-#generalData
-# Load file for Resource Table
-resource <- read_csv(file = here::here("data/ictr_table_resources.csv"))
-
-## Add pricing info on TOPAS
-resource %<>%
- mutate(Price = case_when(Name == "TOPAS" ~ ' Paid/Free',
- TRUE ~ as.character(Price)))
-
-## Add ISIC Archive: Submitted 06/01/2023, 13:31 (vrotemberg@gmail.com)
-new_ISIC <- tibble(
- Name = "ISIC Archive",
- Funding = "Yes",
- Subcategories = "Cancer Imaging",
- `Data Type` = "Clinical imaging",
- `Unique Factors` = "The largest public archive of dermatology photographs. It has around 20 million individual image downloads per month and is widely used for education and AI research.",
- Price = "Free",
- Link = "https://www.isic-archive.com/",
- `Summary` = "The ISIC Archive is an academic-industry collaboration that is devoted to improving dermatology artificial intelligence. It is the largest public archive of images of skin conditions, with special attention to skin cancer detection. We also host grand challenges (and live challenges) for AI models as well as conference workshops.")
-
-## Add new rows to the existing dataset
-new_resource <- resource %>%
- bind_rows(new_ISIC)
-
-## Goal: Create the html version of links in resources
-## Edit 1: Add a column "identifier" to the resource table to use it as a merge key variable with the Data provided column entries in other tables
-## Edit 2: Make sure add new identifiers for new resources in the resource data set.
-resource_identifier <- new_resource %>%
- mutate(identifier = c("PDX", "HemOnc", "ngchm", "OncoMX", "MethCon5", "CIViC", "BioMuta", "TCIA", "SCGV", "ivyGlimpse", "TCPA", "dcmqi", "Region Templates", "Cistrome", "TOPAS", "TCGA", "1000 Genomes", "TARGET", "CCLE", "dbGAP", "CPTAC", "PheKB", "NSCLC Radiomics", "ICGC", "ISIC")) %>% relocate(identifier)
-
-## Save the edited data file
-write.csv(resource_identifier, file = "data/ictr_table_resources_identifier.csv")
-```
-
-## Adding new platforms to the Imaging Table
-
-```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-# imaging <- read_csv(file = here::here("data/ictr_table_imaging.csv"))
-# nameOfCols <- imaging %>% colnames()
-
-## CaPTk: Submitted 06/01/2023, 11:12 (sbakas@upenn.edu)
-new_imaging_CaPTk <- tibble(
- Name = "The Cancer Imaging Phenomics Toolkit (CaPTk)",
- `Link (Hyperlinked Over Name)` = "https://www.med.upenn.edu/cbica/captk/",
- Subcategories = "Radiomics",
- `Unique Factor` = "CaPTk is a stand-alone software client that allows for free image analysis through the Image Processing Portal (IPP) that offers compute power through CaPTk's supporting high performance computing cluster.",
- `Data Types (Clean)` = "Radiographic Imaging",
- Price = "Free",
- Documentation = "https://cbica.github.io/CaPTk/",
- `Data Provided` = "Sample Data available within CaPTk",
- Publications = "https://doi.org/10.1117/1.jmi.5.1.011018",
- `Summary` = "CaPTk is a software platform for analysis of radiographic cancer images, currently focusing on brain, breast, and lung cancer that integrates advanced, validated tools performing various aspects of medical image analysis, that have been developed in the context of active clinical research studies and collaborations toward addressing real clinical needs. CaPTk aims to facilitate the swift translation of advanced computational algorithms into routine clinical quantification, analysis, decision making, and reporting workflow.",
- Funding = "Yes",
- PLink = "https://github.com/CBICA/CaPTk/#downloads")
-
-## Add new rows to the existing dataset
-new_imaging <- read_csv(file = here::here("data/ictr_table_imaging.csv")) %>%
- bind_rows(new_imaging_CaPTk)
-
-## Create new data file
-write.csv(new_imaging, file = "data/ictr_table_imaging_new.csv", row.names = FALSE)
-```
-
-
diff --git a/clinicalTable.Rmd b/clinicalTable.Rmd
index d3fe02a..02dc159 100644
--- a/clinicalTable.Rmd
+++ b/clinicalTable.Rmd
@@ -8,18 +8,12 @@ output: html_document
The following table contains a list of clinical informatics platforms. These platforms work with several types of clinical data, such as EMR Text and Clinical Notes, utilizing Natural Language Processing techniques, AI and machine learning algorithms in order to generate actionable insights with automated research tools.
```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-## edit all the data files before loading them. Compiling this Rmd will generate modified data files.
-knitr::knit_child("alldataFilesEditor.Rmd")
-```
-
-```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-#Load DT, dplyr
library(DT)
-#library(dplyr)
library(here)
library(tidyverse)
library(magrittr)
-#library(RCurl)
+
+source("scripts/format-tables.R")
```
**Table keys:**
@@ -29,131 +23,29 @@ library(magrittr)
```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-# Load file for Clinical Table
-generalData <- read_csv(file = here::here("data/ictr_table_clinical.csv"))
-generalData
-
-# Mutate the tibble to alter three of the columns
-generalData %<>%
- mutate(`Link (Hyperlinked Over Name)` = paste0(' ','
', ''),
- Documentation = paste0(' ','
', ''),
- Publications = paste0(' ','
', ''))
-
-# Mutate generalData's Name to be bolded.
-generalData %<>%
- mutate(Name = paste0('', Name,''))
-
-# Mutate the pricing column to have a link.
-generalData %<>%
- mutate(Price = paste0(' ', Price,''))
-
-# Mutate the tibble to combine all three columns into a general "Platform" column.
-## Awan Edit: Removed line-breaks between linked icons to save space.
-generalData %<>%
- mutate(Platform = paste0(Name, ":",'
'))
-
- generalData[row,"Platform"] <- target
- }
-}
-
-# Shift the location of the "Platform" column.
-generalData %<>%
- relocate(Platform, .after = `Link (Hyperlinked Over Name)`)
-
-# Load file for Resource Table
-resource <- read_csv(file = here::here("data/ictr_table_resources_identifier.csv"))
-
-# Create the html version of links in resources
-## AwanEdit: added a column "identifier" to the resource table to use it as a merge key variable with the Data provided column entries in other tables
-resource <- resource %>%
- mutate(Link = paste0(' ',Name,''))
-## To have shorter acronyms use "identifier" in place of "Name" inside 'mutate'
-
-# # Create a function to merge resources and generalData (edit: This function seems redundant)
-# resourceMerge <- function( generalData,row,col ) {
-# generalData %>%
-# filter(row_number() == row) %>%
-# select(col)
-# }
-
-# Alter the generalData df to see how it interacts with the resources tab.
-# generalData %<>%
-# mutate('Data Provided' = str_replace(string = pull(generalData,'Data Provided'), pattern = "TCGA", replacement = str_subset(string = pull(resource,Link), pattern = "tcga")[1]))
-
-# AwanEdit: Code for Linking Resource table to the other tables' Data Provided column
-LinkUpdater <- bind_cols(Name = pull(generalData, Name),
- read.table(text = as.character(generalData$`Data Provided`), sep = ",", as.is = TRUE, fill = TRUE, na.strings = "")) %>%
- pivot_longer(cols = -Name, names_to = "vars", values_to = "vals") %>%
- filter(!is.na(vals)) %>%
- mutate(vals = str_trim(vals, side = "both")) %>%
- select(-vars, identifier = vals) %>%
- left_join(y = resource %>% select(identifier, Link), by = "identifier") %>%
- mutate(Link = if_else(is.na(Link), identifier, Link)) %>% select(-identifier) %>%
- group_by(Name) %>% mutate(var = paste0("var", 1:n() )) %>% ungroup() %>% relocate(var) %>%
- pivot_wider(names_from = var, values_from = Link) %>%
- unite(col = "Data Provided2", -Name, sep = ", ", na.rm = T, remove = T)
-
-generalData %<>% left_join(LinkUpdater, by = "Name") %>%
- relocate(`Data Provided2`, .before = `Data Provided`) %>%
- select(-`Data Provided`) %>% rename("Data Provided" = `Data Provided2`)
-
-# Create a trimmed version of the data by removing the non-consolidated columns.
-trimmedData <- generalData[ -c(1,2,8,10,12,13) ]
-
-# Shift the location of the "Summary" column.
-trimmedData %<>%
- relocate(Summary, .after = Subcategories)
+# Load file for Clinical Table and make any additions/edits to it here in this block
+clinicalData <- read_csv(file = here::here("data/itcr_table_clinical.csv"))
+```
-# save the trimmed version of the data file to call into allTables.Rmd
-modified_clinical <- trimmedData %>%
- mutate(Category = "Clinical") %>% relocate(Category, .after = Platform)
+```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
+modified_clinical <- formatTheTables(clinicalData, "Clinical", non_resource = TRUE)
# save this data file to the data folder
write_csv(modified_clinical, file = "data/modified_clinical.csv")
```
```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-# Create a Imaging Table
-ITCR_clinical <- trimmedData %>%
- DT::datatable(
- style = 'default',
- width="100%",
- colnames = c('Unique Factor' = 4, 'Types of Data' = 5, 'Summary' = 3),
- rownames = FALSE,
- escape = FALSE,
- #caption = "some caption",
- filter = "top",
- #extensions = list("Scroller")
- options = list(scrollX = TRUE, autoWidth = TRUE, pageLength = 10,
- scrollCollapse = TRUE, fillContainer = TRUE,
- order = (list(0, 'asc')),
- columnDefs = list(list(className = 'dt-center', targets = "_all"),
+# Create a Clinical Table
+
+columnDefsListOfLists <- list(list(className = 'dt-center', targets = "_all"),
list(width = '280px', targets = c(2)) ,
- list(width = '120px', targets = c(3)) ),
- # columnDefs = list(list(width = '300px', targets = c(2)),
- # list(width = '100px', targets = c(4,5)),
- # list(width = '120px', targets = c(0)),
- # list(width = '200px', targets = c(3)),
- # list(width = '150px', targets = "_all")),
- initComplete = JS(
- "function(settings, json) {",
- #"$('body').css({'font-family': 'Calibri'});",
- "$(this.api().table().header()).css({'backgroundColor': '#3f546f'});",
- "$(this.api().table().header()).css({'color': '#fff'});",
- "}"))
- )
+ list(width = '120px', targets = c(3))
+ )
+
+ITCR_clinical <- setup_dt_datatable(modified_clinical, columnDefsListOfLists)
```
```{r,echo=FALSE,message=FALSE, warning=FALSE}
+#Display the clinical table
ITCR_clinical
```
diff --git a/contact.Rmd b/contact.Rmd
index bf04231..071f948 100644
--- a/contact.Rmd
+++ b/contact.Rmd
@@ -16,15 +16,24 @@ output:
```{r, fig.align='center', fig.alt="Banner", out.width="1540px", echo = FALSE}
knitr::include_graphics("resources/images/bannerITCR.png")
```
-
- This file is used to make edits to the data files.
-##
-## ── Column specification ────────────────────────────────────────────────────────
-## cols(
-## Name = col_character(),
-## Funding = col_character(),
-## Subcategories = col_character(),
-## `Data Type` = col_character(),
-## `Unique Factors` = col_character(),
-## Price = col_character(),
-## Link = col_character(),
-## Summary = col_character()
-## )The following table contains a list of general informatics and biomedical platforms that can help researchers work with publicly available data and or their own data. General platforms are those which work with a wide variety of data types, from imaging data to “omics” data, and provide computing resource support across different areas of bioinformatics research.
-Table keys: - = Main Link, = Documentation, = Publications, = ITCR Funded
## Warning: Missing column names filled in: 'X1' [1]The following table contains a list of informatics and biomedical platforms that can help researchers work with multiple types of publicly available data and or their own data. These platforms provide computing resource support across different areas of bioinformatics research.
+The following table contains a list of informatics and biomedical +platforms that can help researchers work with multiple +types of publicly available data and or their own data. These +platforms provide computing resource support across different areas of +bioinformatics research.
Table keys: = Main Link, = Documentation, = Publications, = ITCR Funded
=
+Main Link,
+ = Documentation,
+ =
+Publications, = ITCR
+Funded
',''),
- `Documentation Link` = paste0(' 
', ''),
- Publications = paste0(' 
', ''))
-
-# Mutate the tibble to combine all three columns into a general "Platform" column.
-generalData %<>%
- mutate(Platform = paste0(Name, ":",' ', ''),
- Documentation = paste0(' ',' ', ''),
- Publications = paste0(' ',' ', ''))
-
-# Mutate generalData's Name to be bolded.
-generalData %<>%
- mutate(Name = paste0('', Name,''))
-
-# Mutate the pricing column to have a link.
-generalData %<>%
- mutate(Price = paste0(' ', Price,''))
-
-# Mutate the tibble to combine all three columns into a general "Platform" column.
-## Awan Edit: Removed line-breaks between linked icons to save space.
-generalData %<>%
- mutate(Platform = paste0(Name, ":",' '))
-
- generalData[row,"Platform"] <- target
- }
-}
-
-# Shift the location of the "Platform" column.
-generalData %<>%
- relocate(Platform, .after = `Link (Hyperlinked Over Name)`)
-
-# Load file for Resource Table
-resource <- read_csv(file = here::here("data/ictr_table_resources_identifier.csv"))
-
-# Create the html version of links in resources
-## AwanEdit: added a column "identifier" to the resource table to use it as a merge key variable with the Data provided column entries in other tables
-resource <- resource %>%
- mutate(Link = paste0(' ',identifier,''))
-
-# # Create a function to merge resources and generalData (edit: This function seems redundant)
-# resourceMerge <- function( generalData,row,col ) {
-# generalData %>%
-# filter(row_number() == row) %>%
-# select(col)
-# }
-
-# Alter the generalData df to see how it interacts with the resources tab.
-# generalData %<>%
-# mutate('Data Provided' = str_replace(string = pull(generalData,'Data Provided'), pattern = "TCGA", replacement = str_subset(string = pull(resource,Link), pattern = "tcga")[1]))
-
-# AwanEdit: Code for Linking Resource table to the other tables' Data Provided column
-LinkUpdater <- bind_cols(Name = pull(generalData, Name),
- read.table(text = as.character(generalData$`Data Provided`), sep = ",", as.is = TRUE, fill = TRUE, na.strings = "")) %>%
- pivot_longer(cols = -Name, names_to = "vars", values_to = "vals") %>%
- filter(!is.na(vals)) %>%
- mutate(vals = str_trim(vals, side = "both")) %>%
- select(-vars, identifier = vals) %>%
- left_join(y = resource %>% select(identifier, Link), by = "identifier") %>%
- mutate(Link = if_else(is.na(Link), identifier, Link)) %>% select(-identifier) %>%
- group_by(Name) %>% mutate(var = paste0("var", 1:n() )) %>% ungroup() %>% relocate(var) %>%
- pivot_wider(names_from = var, values_from = Link) %>%
- unite(col = "Data Provided2", -Name, sep = ", ", na.rm = T, remove = T)
-
-generalData %<>% left_join(LinkUpdater, by = "Name") %>%
- relocate(`Data Provided2`, .before = `Data Provided`) %>%
- select(-`Data Provided`) %>% rename("Data Provided" = `Data Provided2`)
-
-# Create a trimmed version of the data by removing the non-consolidated columns.
-trimmedData <- generalData[ -c(1,2,8,10,12,13) ]
-
-# Shift the location of the "Summary" column.
-trimmedData %<>%
- relocate(Summary, .after = Subcategories)
+# Load file for omics Table and make any edits/additions in this block
+omicsData <- read_csv(file = here::here("data/itcr_table_omics.csv"))
+
+#While reworking the code, saw that ICGC and PCAWG were not separated by a comma and therefore ICGC wasn't linked
+tibbleCGC <- tibble(
+ Name = "Cancer Genome Collaboratory",
+ `Data Provided` = "ICGC, PCAWG, DCC"
+)
+
+omicsData <- dplyr::rows_update(omicsData, tibbleCGC, by = "Name")
+
+```
+
+```{r, echo=FALSE,results='hide',message=FALSE, warning=FALSE}
+
+modified_omics <- formatTheTables(omicsData, "Omics", non_resource = TRUE)
# save the trimmed version of the data file to call into allTables.Rmd
-modified_omics <- trimmedData %>%
- mutate(Category= "Omics") %>% relocate(Category, .after = Platform)
-# save this data file to the data folder
write_csv(modified_omics, file = "data/modified_omics.csv")
```
```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-# Create a Imaging Table
-ITCR_omics <- trimmedData %>%
- DT::datatable(
- style = 'default',
- width="100%",
- colnames = c('Unique Factor' = 4, 'Types of Data' = 5, 'Summary' = 3),
- rownames = FALSE,
- escape = FALSE,
- #caption = "some caption",
- filter = "top",
- #extensions = list("Scroller")
- options = list(scrollX = TRUE, autoWidth = TRUE, pageLength = 10,
- scrollCollapse = TRUE, fillContainer = TRUE,
- order = (list(0, 'asc')),
- columnDefs = list(list(className = 'dt-center', targets = "_all"),
+# Create an omics Table
+
+columnDefsListOfLists <- list(list(className = 'dt-center', targets = "_all"),
list(width = '280px', targets = c(2)) ,
- list(width = '130px', targets = c(3)) ),
- # columnDefs = list(list(width = '300px', targets = c(2)),
- # list(width = '100px', targets = c(4,5)),
- # list(width = '120px', targets = c(0)),
- # list(width = '200px', targets = c(3)),
- # list(width = '150px', targets = "_all")),
- initComplete = JS(
- "function(settings, json) {",
- #"$('body').css({'font-family': 'Calibri'});",
- "$(this.api().table().header()).css({'backgroundColor': '#3f546f'});",
- "$(this.api().table().header()).css({'color': '#fff'});",
- "}"))
- )
+ list(width = '130px', targets = c(3)) )
+
+ITCR_omics <- setup_dt_datatable(modified_omics, columnDefsListOfLists)
```
```{r,echo=FALSE,message=FALSE, warning=FALSE}
+# Display the omics table
ITCR_omics
```
diff --git a/otherTable.Rmd b/otherTable.Rmd
deleted file mode 100644
index d552b7d..0000000
--- a/otherTable.Rmd
+++ /dev/null
@@ -1,77 +0,0 @@
----
-title: "**Non-Specified Informatics Table**"
-output: html_document
----
-
-### **About**
-
-This website contains a list of non-specified informatics tools funded by ITCR grants.
-
-```{r,echo=FALSE,results='hide',message=FALSE}
-#Load DT, dplyr
-library(DT)
-library(dplyr)
-library(here)
-library(tidyverse)
-library(magrittr)
-#library(RCurl)
-```
-
-```{r,echo=FALSE,results='hide',message=FALSE}
-# Load file for Imaging Table
-generalData <- read_csv(file = here::here("data/ictr_table_other.csv"))
-generalData
-
-# Mutate the tibble to alter three of the columns
-generalData %<>%
- mutate(`Link (Hyperlinked Over Name)` = paste0(' ',''),
- `Documentation Link` = paste0(' ', ''),
- Publications = paste0(' ', ''))
-
-# Mutate the tibble to combine all three columns into a general "Platform" column.
-generalData %<>%
- mutate(Platform = paste0(Name, ":",' = ITCR Funded
- '))
-
- generalData[row,"Name"] <- target
- }
-}
-
-# Create a trimmed version of the data by removing the non-consolidated columns.
-trimmedData <- generalData[ -c(1, 2, 4, 9) ]
-## if data is loaded from original ictr_table_resources.csv, only remove columns 2 and 7 generalData[ -c(2, 7) ]
-trimmedData
-
-# Shift the location of the "Summary" column.
-trimmedData %<>%
- relocate(Summary, .after = Subcategories) %>% relocate(`Unique Factors`, .after = Summary)
-```
-
-```{r,echo=FALSE,results='hide',message=FALSE, warning=FALSE}
-# Create a Imaging Table
-ITCR_resource <- trimmedData %>%
- DT::datatable(
- style = 'default',
- width="100%",
- colnames = c('Unique Factor' = 4, 'Types of Data' = 5, 'Summary' = 3),
- rownames = FALSE,
- escape = FALSE,
- #caption = "some caption",
- filter = "top",
- #extensions = list("Scroller")
- options = list(scrollX = TRUE, autoWidth = TRUE, pageLength = 10,
- scrollCollapse = TRUE, fillContainer = TRUE,
- order = (list(0, 'asc')),
- columnDefs = list(list(className = 'dt-center', targets = "_all"),
- list(width = '120px', targets = c(0)) ,
- list(width = '300px', targets = c(2)) ,
- list(width = '140px', targets = c(3)) ,
- list(width = '100px', targets = c(4)) ),
- # columnDefs = list(list(width = '300px', targets = c(2)),
- # list(width = '100px', targets = c(4,5)),
- # list(width = '120px', targets = c(0)),
- # list(width = '200px', targets = c(3)),
- # list(width = '150px', targets = "_all")),
- initComplete = JS(
- "function(settings, json) {",
- #"$('body').css({'font-family': 'Calibri'});",
- "$(this.api().table().header()).css({'backgroundColor': '#3f546f'});",
- "$(this.api().table().header()).css({'color': '#fff'});",
- "}"))
- )
-```
-
-```{r,echo=FALSE,message=FALSE, warning=FALSE}
-ITCR_resource
-```
diff --git a/scripts/format-tables.R b/scripts/format-tables.R
new file mode 100644
index 0000000..14184e6
--- /dev/null
+++ b/scripts/format-tables.R
@@ -0,0 +1,151 @@
+#!/usr/bin/env Rscript
+
+library(magrittr)
+library(tidyverse)
+library(DT)
+library(here)
+
+#' Format the tibble/table to bold names, link links, add icons, and rearrange/select columns
+#'
+#' @param tableOI a tibble
+#' @param keywordOI a string; only necessary if non_resource is TRUE; example is "Clinical" or "Omics"
+#' @param non_resource a boolean; default is FALSE; whether or not the table being formatted is the resource table or a tools table; if non_resource true, it's a tool's table; if false, the resource table.
+#'
+#' @return
+
+formatTheTables <- function(tableOI, keywordOI, non_resource = FALSE){
+
+ #check that it's tibble, if not, make it a tibble
+ if (!is_tibble(tableOI)){
+ tableOI <- as_tibble(test_df)
+ }
+
+ #Mutate the tibble to alter three of the columns
+ if (non_resource) {
+ generalData <- tableOI %>%
+ mutate(`Link (Hyperlinked Over Name)` = paste0(' ',' ', ''),
+ Documentation = paste0(' ',' ', ''),
+ Publications = paste0(' ',' ', ''))
+ } else {
+ generalData <- tableOI %>%
+ mutate(Name = paste0(' ',Name,''))
+ }
+
+ #Mutate generalData's Name to be bolded.
+ generalData %<>%
+ mutate(Name = paste0('', Name, ""))
+
+ #Mutate the pricing column to have a link & Mutate the tibble to combine all three columns into a general "Platform" column.
+ if (non_resource){
+ generalData %<>%
+ mutate(Price = paste0(' ', Price,'')) %>%
+ mutate(Platform = paste0(Name, ":",''))
+
+ generalData[row, "Platform"] <- target
+ }
+ }
+
+ generalData %<>%
+ relocate(Platform, .after = `Link (Hyperlinked Over Name)`)
+
+ resource <- read_csv(file = here::here("data/itcr_table_resources_identifier.csv"))
+
+ resource %<>%
+ mutate(Link = paste0(' ',identifier,''))
+
+ LinkUpdater <- bind_cols(Name = pull(generalData, Name),
+ read.table(text = as.character(generalData$`Data Provided`), sep = ",",
+ as.is = TRUE, fill = TRUE, na.strings = "")) %>%
+ pivot_longer(cols = -Name, names_to = "vars", values_to = "vals") %>%
+ filter(!is.na(vals)) %>%
+ mutate(vals = str_trim(vals, side = "both")) %>%
+ select(-vars, identifier = vals) %>%
+ left_join(y = resource %>% select(identifier, Link), by = "identifier") %>%
+ mutate(Link = if_else(is.na(Link), identifier, Link)) %>%
+ select(-identifier) %>%
+ group_by(Name) %>% mutate(var = paste0("var", 1:n() )) %>% ungroup() %>%
+ relocate(var) %>%
+ pivot_wider(names_from = var, values_from = Link) %>%
+ unite(col = "Data Provided2", -Name, sep = ", ", na.rm = T, remove = T)
+
+ generalData %<>% left_join(LinkUpdater, by = "Name") %>%
+ relocate(`Data Provided2`, .before = `Data Provided`) %>%
+ select(-`Data Provided`) %>% rename("Data Provided" = `Data Provided2`)
+
+ } else {
+ for (row in 1:nrow(generalData)) {
+ status <- generalData[row, "Funding"]
+ target <- generalData[row, "Name"]
+
+ if(status == "Yes") {
+ target %<>%
+ mutate(Name = paste0(Name, ''))
+
+ generalData[row, "Name"] <- target
+ }
+ }
+ }
+
+ #Create a trimmed version of the data by removing the non-consolidated columns
+ ##For non-resource Table want to keep columns "Platform", "Subcategories", "Unique Factor", "Data Types (Clean)", "Price", "Data Provided", "Summary"
+ ##For Resource Table Want to keep columns "Name", "Subcategories", "Summary", "Unique Factors", "Data Type", and "Price"
+ if (non_resource){
+ trimmedData <- generalData[ c("Platform", "Subcategories", "Unique Factor", "Data Types (Clean)", "Price", "Data Provided", "Summary")] %>%
+ relocate(Summary, .after = Subcategories) %>%
+ mutate(Category = keywordOI) %>%
+ relocate(Category, .after = Platform)
+ } else {
+ trimmedData <- generalData[ c("Name", "Subcategories", "Data Type", "Unique Factors", "Price", "Summary") ] %>%
+ relocate(Summary, .after = Subcategories) %>%
+ relocate(`Unique Factors`, .after = Summary)
+ }
+
+ return(trimmedData)
+}
+
+#' Create an HTML table using the DT::datatable function
+#'
+#' @param modified_data a tibble; has been formatted to rearrange columns, etc. already
+#' @param columnDefsListOfLists a list of lists; passed to columnDefs; user sets various attributes for columns, each sub-list must contain a vector named targets, specifying the applied columns; we're using it to set column widths and center entries
+#'
+#' @return ITCR_table a formatted DT::datatable
+
+
+setup_dt_datatable <- function(modified_data, columnDefsListOfLists){
+ ITCR_table <- modified_data %>%
+ select(-any_of("Category")) %>%
+ DT::datatable(
+ style = 'default',
+ width="100%",
+ colnames = c('Unique Factor' = 4, 'Types of Data' = 5, 'Summary' =3),
+ rownames = FALSE,
+ escape = FALSE,
+ filter = "top",
+ options = list(scrollX = TRUE, autoWidth = TRUE, pageLength = 10,
+ scrollCollapse = TRUE, fillContainer = TRUE,
+ order = (list(0, 'asc')),
+ columnDefs = columnDefsListOfLists,
+ initComplete = JS(
+ "function(settings, json) {",
+ #"$('body').css({'font-family': 'Calibri'});",
+ "$(this.api().table().header()).css({'backgroundColor': '#3f546f'});",
+ "$(this.api().table().header()).css({'color': '#fff'});",
+ "}")
+ )
+ )
+ return(ITCR_table)
+}
\ No newline at end of file