Initial commit

Author: William Ryan

.Rprofile

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+source("renv/activate.R")

.gitignore

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+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store
+_bookdown_files
+_book
+packages.bib
+.quarto
+_site
+.Rapp
+.Rapp.history
+/.quarto/

MultiomicMenu.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX

_common.R

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+### Below is quarto voodoo to make sure the environment is saved and loaded between pages, because quarto is KM, not MK
+
+#Load common environment if it exists
+if (file.exists(here::here("data/env.RData"))) {
+  load(here::here("data/env.RData"))
+}
+
+#Hook knitr to save common environment on each document render end
+local({
+  hook_old <- knitr::knit_hooks$get("document") #Grab current hook
+  knitr::knit_hooks$set(
+    document = function(x) {
+      save.image(file = here::here("data/env.RData")) #Save environment
+      hook_old(x) #Important: call the original hook, or everything will break
+    }
+  )
+})
+
+### End of quarto voodoo
+
+###Helper lines may be uncommented to install packages manually!
+
+# if (!require("BiocManager", quietly = TRUE))
+#   install.packages("BiocManager")
+#
+# BiocManager::install("org.Hs.eg.db", force = TRUE)
+# BiocManager::install("topGO", force = TRUE)
+# renv::install("IOR-Bioinformatics/PCSF", force = TRUE)
+# renv::install("CogDisResLab/Kinograte", force = TRUE)
+
+###Load all packages statistically for renv
+suppressPackageStartupMessages({
+  library(here)
+  library(babelgene)
+  library(tidyverse)
+  library(kinograte)
+  library(HGNChelper)
+  library(creedenzymatic)
+  library(DT)
+  library(htmltools)
+  library(enrichR)
+  library(ggnetwork)
+  library(igraph)
+  library(intergraph)
+  library(network)
+  library(scatterpie)
+  library(fgsea)
+  library(PAVER)
+  library(ggprism)
+  library(svglite)
+  library(httr)
+  library(jsonlite)
+})
+
+knitr::opts_chunk$set(
+  comment = "#>",
+  cache = FALSE,
+  echo = FALSE,
+  message = FALSE,
+  warning = FALSE
+)
+
+options(readr.show_col_types = FALSE)
+
+set.seed(123)
+
+# Quiet any noisy function
+quiet <- function(x) {
+  sink(tempfile())
+  on.exit(sink())
+  invisible(force(x))
+}
+
+# Make a formatted HTML table
+make_table <- function(df, caption=NULL) {
+  DT::datatable(
+    df,
+    rownames = FALSE,
+    caption = tags$caption(style = 'text-align: left;', caption),
+    options = list(
+      scrollX = TRUE,
+      scrollY = TRUE,
+      paging = TRUE,
+      fixedHeader = TRUE,
+      pageLength = 10
+    )
+  ) %>% formatStyle(names(df), "white-space" = "nowrap")
+}

_quarto.yml

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+project:
+  type: website
+  render:
+       - index.qmd
+       - learn.qmd
+       - data.qmd
+       - pathways.qmd
+
+website:
+  title: "MultiomicMenu"
+  navbar:
+    left:
+      - href: index.qmd
+        text: Home
+      - learn.qmd
+      - data.qmd
+      - pathways.qmd
+
+format:
+  html:
+    theme: cosmo
+    css: styles.css
+    toc: true
+
+editor: source
+