Adding ARAMIS and ARAMISPCTG templates

R/epurate.R

@@ -84,3 +84,86 @@ QIMR <- function(toc = TRUE, code_folding = "hide", number_sections=TRUE) {
                                code_folding = code_folding,
                             )
 }
+
+# Features of ARAMIS Template
+ARAMIS <- function(toc = TRUE, code_folding = "hide", number_sections=TRUE) {
+
+  # get the locations of resource files located within the package
+  css <- system.file("rmarkdown", "templates", "ARAMIS" ,"resources", "style.css", package = "epuRate")
+  template <- system.file("rmarkdown", "templates", "ARAMIS" ,"resources", "template_aramis.html", package = "epuRate")
+
+  # call the base html_document function
+  rmarkdown::html_document( theme= "lumen",
+                               template= template,
+                               css= css,
+                               toc= toc,
+                               toc_float = TRUE,
+                               toc_depth = 2,
+                               number_sections= number_sections,
+                               df_print = "paged",
+                               code_folding = code_folding,
+                            )
+}
+
+
+# Features of ARAMIS+PCTG Template
+ARAMISPCTG <- function(toc = TRUE, code_folding = "hide", number_sections=TRUE) {
+
+  # get the locations of resource files located within the package
+  css <- system.file("rmarkdown", "templates", "ARAMISPCTG" ,"resources", "style.css", package = "epuRate")
+  template <- system.file("rmarkdown", "templates", "ARAMISPCTG" ,"resources", "template_aramispctg.html", package = "epuRate")
+
+  # call the base html_document function
+  rmarkdown::html_document( theme= "lumen",
+                               template= template,
+                               css= css,
+                               toc= toc,
+                               toc_float = TRUE,
+                               toc_depth = 2,
+                               number_sections= number_sections,
+                               df_print = "paged",
+                               code_folding = code_folding,
+                            )
+}
+
+
+# Features of KCL Template
+KCL <- function(toc = TRUE, code_folding = "hide", number_sections=TRUE) {
+
+  # get the locations of resource files located within the package
+  css <- system.file("rmarkdown", "templates", "KCL" ,"resources", "style.css", package = "epuRate")
+  template <- system.file("rmarkdown", "templates", "KCL" ,"resources", "template_kcl.html", package = "epuRate")
+
+  # call the base html_document function
+  rmarkdown::html_document( theme= "lumen",
+                               template= template,
+                               css= css,
+                               toc= toc,
+                               toc_float = TRUE,
+                               toc_depth = 2,
+                               number_sections= number_sections,
+                               df_print = "paged",
+                               code_folding = code_folding,
+                            )
+}
+
+
+# Features of International Statistical Genetics Workshop (Boulder workshop) Template
+ISGW <- function(toc = TRUE, code_folding = "hide", number_sections=TRUE) {
+
+  # get the locations of resource files located within the package
+  css <- system.file("rmarkdown", "templates", "ISGW" ,"resources", "style.css", package = "epuRate")
+  template <- system.file("rmarkdown", "templates", "ISGW" ,"resources", "template_ISGW.html", package = "epuRate")
+
+  # call the base html_document function
+  rmarkdown::html_document( theme= "lumen",
+                               template= template,
+                               css= css,
+                               toc= toc,
+                               toc_float = TRUE,
+                               toc_depth = 2,
+                               number_sections= number_sections,
+                               df_print = "paged",
+                               code_folding = code_folding,
+                            )
+}

README.md

@@ -19,6 +19,9 @@ Note that a specific version is available for:
 - members of the [University of Queensland](https://holtzy.github.io/epuRate/uq.html)
 - members of [PCTG](https://holtzy.github.io/epuRate/pctg.html)
 - members of [QIMR](https://holtzy.github.io/epuRate/qimr.html)
+- members of [ARAMIS]
+- members of [KCL (King's College London)]
+- members of [ISGW (International Statistical Genetics Workshop)]
 
 
 <br><br><br>
@@ -28,17 +31,37 @@ Using it
 - Install the R package:
 ```
 library(devtools)
-install_github("holtzy/epuRate")
+install_github("holtzy/epuRate") # For standard, UQ, PCTG and QIMR templates
+install_github("baptisteCD/epuRate") # For all of the above as well as ARAMIS lab, KCL (King's College London), ISGW (International Statistical Genetics Workshop)
 library(epuRate)
 ```
 - Open a new rmd file in Rstudio: File -> New File -> R Markdown -> From Template -> epuRate.
 
 - Change  the Header of your document with your name, email adress, github / twitter / linkedIn details if you want to display them. You can also add a logo over the table of content.
 
 
+<br><br><br>
+Personalised version
+--------
+- Fork the repo and pull on your local computer
+- Duplicate one of the template folders (**/epuRate/inst/rmarkdown/templates/**)
+- Rename the template folder: **MYNEWTEMPLATE**
+- Modify the template name in the file **template.yaml**
+- Replace the logo file (jpg, png) in **/epuRate/inst/rmarkdown/templates/MYNEWTEMPLATE/resources/**
+- Add path to this logo file  at line 382 of the **template_MYNEWTEMPLATE.html** file
+- The path should correspond to your github link to the logo so typically: **https://github.com/MYGITHUBUSERNAME/epuRate/raw/master/inst/rmarkdown/templates/MYNEWTEMPLATE/resources/MYNEWTEMPLATE.png**
+- Choose the personalised color that suits your logo and add the HEX code to the **style.css** file
+- I tend to use a color from the logo, which I obtain using free online tool(s)
+- You can choose a palette of colours or a single colour for the titles, links, TOCs and buttons
+- In the **epuRate/R/epurate.R** add an instance for your new template and select the default options of the RMarkdown
+- Commit and push the changes into your forked version in Github
+- You should now be able to use your template by running **install_github("MYGITHUBUSERNAME/epuRate")**
 
-
+
+--> Alternatively email me or send me a message on github with your **logo file**, the **HEX color code**
+ and the **Name of your wished template**, and I will see what I can do.
+
 <br><br><br>
 Acknowledgment
 --------
-Thanks to [Florian Rohart](http://florian.rohart.free.fr/Professional_page/Home.html) for his help on the PCTG template. Thanks to [Rstudio](https://www.rstudio.com) and its team for developing so many awesome tools.
+Thanks to [Florian Rohart](http://florian.rohart.free.fr/Professional_page/Home.html) for his help on the PCTG template and [Baptiste Couvy-Duchesne](https://github.com/baptisteCD) for extending the template to ARAMIS, KCL and ISGW. Thanks to [Rstudio](https://www.rstudio.com) and its team for developing so many awesome tools.

build.R

@@ -5,9 +5,14 @@
 # Remove previous version just in Case
 remove.packages("epuRate")
 
-# Install with devtools
+# Install with devtools (LOCAL)
+#library(devtools)
+#devtools::install("../epuRate")
+
+# Install from github
 library(devtools)
-devtools::install("../epuRate")
+devtools::install_github("baptisteCD/epuRate")
+
 
 # Load to check it is all good
 library(epuRate)

epuRate.Rproj

@@ -5,8 +5,13 @@ SaveWorkspace: No
 AlwaysSaveHistory: Default
 
 EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
 Encoding: UTF-8
 
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
 AutoAppendNewline: Yes
 StripTrailingWhitespace: Yes
 

inst/rmarkdown/templates/ARAMIS/resources/style.css

@@ -0,0 +1,87 @@
+h1, .h1, h2, .h2, h3, .h3 {
+    margin-top: 84px;
+    color: #6A0888
+}
+
+h1 {
+  padding-top: 100px;
+}
+
+h1.title {
+  text-align: center;
+}
+
+pre {
+    border: 0px solid #cccccc;
+    border-radius: 0px;
+ }
+
+
+
+
+
+
+
+/* ---------- Links ----------------- */
+a {
+  color: #6A0888;
+}
+a:hover {
+  color: #6A0888;
+}
+
+
+
+
+/* ---------- TOC ----------------- */
+#TOC {
+  top: 30%;
+  position: fixed;
+  width: 210px;
+}
+.tocify {
+  border: none;
+  color: grey;
+  border-radius: 0px;
+}
+.list-group-item.active {
+    color: #6A0888;
+    background-color: white;
+    border-left: solid;
+    border-color: #6A0888;
+}
+.list-group-item:hover {
+    color: #6A0888;
+    background-color: white;
+    border-left: solid;
+    border-color: #6A0888;
+}
+.tocify-extend-page {
+  display: none;
+}
+
+
+/* ------ This is just to fix the bug on Safari where table of content is on top of content */
+.toc-content {
+  margin-left: 230px
+}
+
+
+
+
+/* ---------- Button ----------------- */
+.btn {
+    border-width: 0 0px 0px 0px;
+    font-weight: normal;
+    text-transform: ;
+    color: #6A0888;
+}
+.btn-default {
+    color: #6A0888;
+    background-color: #ffffff;
+    border-color: #ffffff;
+}
+
+.nav-pills > li.active > a, .nav-pills > li.active > a:hover, .nav-pills > li.active > a:focus {
+    background-color: #6A0888;
+}