Changed description for new cluster data

.github/workflows/docker-image.yml

@@ -0,0 +1,44 @@
+name: Create and publish a Docker image to ghcr.io
+
+on:
+  push:
+    branches:
+      - main
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            type=raw,value={{date 'YYYYMMDD-HHmmss' tz='Europe/Stockholm'}}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

app/Dockerfile → Dockerfile

@@ -6,22 +6,25 @@ RUN apt-get update && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
+
+RUN mkdir /home/data \
+    && chown -R shiny:shiny /home/data
+COPY /data/ /home/data/
+
+COPY /start-script.sh ./start-script.sh
+RUN chmod +x ./start-script.sh
+
+RUN rm -rf /srv/shiny-server/*
+COPY /app/ /srv/shiny-server/
+
 # Command to install standard R packages from CRAN; enter the list of required packages for your app here
 RUN Rscript -e 'install.packages(c("shiny","tidyverse","BiocManager", "Seurat", "DT", "dplyr", "ggplot2", "SeuratObject"), dependencies=TRUE)'
 
 # Command to install packages from Bioconductor; enter the list of required Bioconductor packages for your app here
 RUN Rscript -e 'BiocManager::install(c("Biostrings"),ask = F)'
 
-RUN rm -rf /srv/shiny-server/*
-COPY ./ /srv/shiny-server/
-
-# Make sure permissions are set so that the shiny user can read/write to the app directory.
-# This assumes that there is a 'data' directory within './' that you reference in your Shiny app.
-RUN chown -R shiny:shiny /srv/shiny-server && \
-    chmod -R 755 /srv/shiny-server
-
 USER shiny
 
 EXPOSE 3838
 
-CMD ["/usr/bin/shiny-server"]
+ENTRYPOINT ["./start-script.sh"]

app/app.R

@@ -82,15 +82,15 @@ ui <- fluidPage(
                     DT::dataTableOutput(outputId = 'deg_table')
                 ),
                 tabPanel('DEGs 2024 feeding',
-                h4('Differentially Expressed Genes between selected clusters (leiden clustering resolution 0.6) for variable "feeding"'),
-                p('Differentially expressed genes between one cluster and all others. Columns: **avg_log2FC**: Average log2 fold Change in expression,
+                h4('Differentially Expressed Genes for selected clusters (leiden clustering resolution 0.6) between conditions 'fed' and 'starved' for variable "feeding"'),
+                p('Differentially expressed genes between 'fed' and 'starved' for respective cluster. Columns: **avg_log2FC**: Average log2 fold Change in expression,
                     **pct.1**: Percentage of cells in respective cluster expressing the gene, **pct.2***: percentage of all other cells expressing the gene,
                     **p_val_adjust**: Adjusted p-value after correction for multiple testing, **cluster**: cluster number'),
                     DT::dataTableOutput(outputId = 'deg_table_2024_feeding')
                 ),
                 tabPanel('DEGs 2024 beta-cells',
-                h4('Differentially Expressed Genes between selected clusters (leiden clustering resolution 0.6) for variable "beta_cells"'),
-                p('Differentially expressed genes between one cluster and all others. Columns: **avg_log2FC**: Average log2 fold Change in expression,
+                h4('Differentially expressed genes for selected clusters (leiden clustering resolution 0.6) between conditions 'ablated' and 'non-ablated' for variable "beta_cells"'),
+                p('Differentially expressed genes between 'ablated' and 'non-ablated' for respective cluster. Columns: **avg_log2FC**: Average log2 fold Change in expression,
                     **pct.1**: Percentage of cells in respective cluster expressing the gene, **pct.2***: percentage of all other cells expressing the gene,
                     **p_val_adjust**: Adjusted p-value after correction for multiple testing, **cluster**: cluster number'),
                     DT::dataTableOutput(outputId = 'deg_table_2024_beta')
@@ -107,21 +107,21 @@ server <- function(input, output) {
     observe({
 
         #Read in distinct seurat objects
-        seurat_objects$complete_2023 <- readRDS("data/2023_complete_filtered_norm_scaled.rds")
-        seurat_objects$'2023_ablated' <- readRDS("data/2023_ablated_filtered_norm_scaled.rds")
-        seurat_objects$'2023_nonablated' <- readRDS("data/2023_nonablated_filtered_norm_scaled.rds")
+        seurat_objects$complete_2023 <- readRDS("/home/data/2023_complete_filtered_norm_scaled.rds")
+        seurat_objects$'2023_ablated' <- readRDS("/home/data/2023_ablated_filtered_norm_scaled.rds")
+        seurat_objects$'2023_nonablated' <- readRDS("/home/data/2023_nonablated_filtered_norm_scaled.rds")
 
-        seurat_objects$complete_2024 <- readRDS("data/2024_complete_filtered_norm_scaled.rds")
-        seurat_objects$'2024_ablated' <- readRDS("data/2024_ablated_filtered_norm_scaled.rds")
-        seurat_objects$'2024_nonablated' <- readRDS("data/2024_nonablated_filtered_norm_scaled.rds")
-        seurat_objects$'2024_fed' <- readRDS("data/2024_fed_filtered_norm_scaled.rds")
-        seurat_objects$'2024_starved' <- readRDS("data/2024_starved_filtered_norm_scaled.rds")
+        seurat_objects$complete_2024 <- readRDS("/home/data/2024_complete_filtered_norm_scaled.rds")
+        seurat_objects$'2024_ablated' <- readRDS("/home/data/2024_ablated_filtered_norm_scaled.rds")
+        seurat_objects$'2024_nonablated' <- readRDS("/home/data/2024_nonablated_filtered_norm_scaled.rds")
+        seurat_objects$'2024_fed' <- readRDS("/home/data/2024_fed_filtered_norm_scaled.rds")
+        seurat_objects$'2024_starved' <- readRDS("/home/data/2024_starved_filtered_norm_scaled.rds")
 
         #Read in DEGs
-        seurat_objects$DEGs_2023 <- readRDS('data/DEGs_2023.rds')
-        seurat_objects$DEGs_2024 <- readRDS('data/DEGs_2024.rds')
-        seurat_objects$DEGs_2024_beta_cells <- readRDS('data/2024_leiden06_beta_DEGs.rds')
-        seurat_objects$DEGs_2024_feeding <- readRDS('data/2024_leiden06_feed_DEGs.rds')
+        seurat_objects$DEGs_2023 <- readRDS('/home/data/DEGs_2023.rds')
+        seurat_objects$DEGs_2024 <- readRDS('/home/data/DEGs_2024.rds')
+        seurat_objects$DEGs_2024_beta_cells <- readRDS('home/data/2024_leiden06_beta_DEGs.rds')
+        seurat_objects$DEGs_2024_feeding <- readRDS('home/data/2024_leiden06_feed_DEGs.rds')
     })  
 
     # Create a reactive expression for a subset of genes
@@ -342,4 +342,4 @@ server <- function(input, output) {
 
     }
 
-shinyApp(ui = ui, server = server)
+shinyApp(ui = ui, server = server)

start-script.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+/usr/bin/shiny-server