add docker - file

Dockerfile

@@ -0,0 +1,50 @@
+FROM r-base
+
+# system libraries of general use
+## install debian packages
+RUN apt-get update -qq && apt-get -y --no-install-recommends install \
+libxml2-dev \
+libcairo2-dev \
+libsqlite3-dev \
+libmariadbd-dev \
+libpq-dev \
+libssh2-1-dev \
+unixodbc-dev \
+libcurl4-openssl-dev \
+libssl-dev
+
+## update system libraries
+RUN apt-get update && \
+apt-get upgrade -y && \
+apt-get clean
+
+
+## renv.lock file
+# COPY /example-app/renv.lock ./renv.lock
+
+# install renv & restore packages
+RUN Rscript -e 'install.packages("renv")'
+RUN Rscript -e 'install.packages("shiny")'
+RUN Rscript -e 'install.packages("ggplot2")'
+RUN Rscript -e 'install.packages("Seurat")'
+RUN Rscript -e 'install.packages("ggplot2")'
+RUN Rscript -e 'install.packages("dplyr")'
+RUN Rscript -e 'install.packages("markdown")'
+RUN Rscript -e 'install.packages("tidyr")'
+RUN Rscript -e 'renv::consent(provided = TRUE)'
+RUN Rscript -e 'renv::restore()'
+RUN Rscript -e 'memory.limit(size=20000)'
+
+
+# copy necessary files
+## app folder
+COPY app.R /app.R
+COPY Keller_more_clusterings.rds /Keller_more_clusterings.rds
+COPY README.md /README.md
+
+
+# run app on container start
+CMD ["Rscript", "-e", "shiny::runApp('/app.R', host = '0.0.0.0', port = 3838)"]
+
+# expose port
+EXPOSE 3838

README.md

@@ -1,6 +1,14 @@
 ---
 Shiny App Tutorial
 ---
+### Local Install Directions:
+1. Install docker on your computer
+2. git clone 
+3. Move in RDS file of interest.
+4. Edit the read RDS line in `app.R` file to be `/example_app/{your rds file name}`
+4. `docker-compose build`
+5. `docker-compose up`
+
 
 ### TODO list:
 - fix the violin plot ordering

app.R

@@ -8,11 +8,13 @@ library(tidyr)
 # Some initial setup:
 # this will not work if underscores are in the orig.ident (only for some views)
 # take in the file, get list of genes, get metadata numbers and categories, get pcs 1-9, and factors..
-aggregate <- readRDS('/Users/keithmitchell/Desktop/Repositories/haudenschild/keith_analysis_round2/HaudenschildRound2_celltype_LR_DIGEST.rds')
+aggregate <- readRDS('Keller_more_clusterings.rds')
 genes = aggregate@assays$RNA
 reductions <- attributes(aggregate@reductions)
 meta_nums <- colnames(dplyr::select_if(aggregate@meta.data, is.numeric))
 meta_cats <- c(colnames(dplyr::select_if(aggregate@meta.data, is.character)), colnames(dplyr::select_if(aggregate@meta.data, is.factor)),colnames(dplyr::select_if(aggregate@meta.data, is.logical)))
+meta_cats <- meta_cats[meta_cats != "orig.ident"]
+mysplitbydefault <- "Health"
 pcs <- list('PC_1','PC_2','PC_3','PC_4','PC_5','PC_6','PC_7','PC_8','PC_9')
 use.pcs <- 1:50
 #agg_cats <- colnames(dplyr::select_if(aggregate@meta.data, is.factor))
@@ -258,7 +260,7 @@ server = function(input, output, session){
     order <- sort(levels(aggregate))
     levels(aggregate) <- order
     DimPlot(aggregate, reduction=input$reduction_seperated_categorical,
-            split.by = "orig.ident", ncol=4
+            split.by = mysplitbydefault, ncol=4
     )
   })
 
@@ -268,7 +270,7 @@ server = function(input, output, session){
     order <- sort(levels(aggregate))
     levels(aggregate) <- order
     DimPlot(aggregate, reduction=input$reduction_seperated_categorical,
-            split.by = "orig.ident", ncol=4
+            split.by = mysplitbydefault, ncol=4
     )
   })
 
@@ -328,10 +330,10 @@ server = function(input, output, session){
     else{widedat <- FetchData(aggregate, marker)}
 
     widedat$Cluster <- Idents(aggregate)
-    widedat$orig.ident = eval(call("$", aggregate, input$identity_seperated2))
-    widedat$final = paste(widedat$orig.ident, widedat$Cluster, sep="_")
+    widedat[[mysplitbydefault]] = eval(call("$", aggregate, input$identity_seperated2))
+    widedat$final = paste(widedat[[mysplitbydefault]], widedat$Cluster, sep="_")
     final_object = (aggregate(widedat[, 1:2], list(widedat$final), mean)[1:2])
-    lab_list = widedat$orig.ident
+    lab_list = widedat[[mysplitbydefault]]
     identities = widedat$Cluster
 
     num_list = widedat[[marker]]