shiny

rMATS-long shiny

About

A shiny server for visualizing rMATS-long results

Table of Contents

• Dependencies
• Usage
  • Data
  • Shiny App
  • Example

Dependencies

For the shiny app, the dependencies for rMATS-long are needed as well as the r-shiny and r-bslib packages. The rMATS-long dependencies can be installed to a conda environment by running ../install. Then the additional packages can be installed:

cd rMATS-long
./install
conda activate ./conda_env
conda install -c conda-forge -c bioconda --file ./shiny/conda_requirements.txt

The shiny server can be run when the conda environment is activated

Usage

Data

The app will prompt for an rMATS-long output directory. From that directory, it will attempt to find files and directories named like the output from the main rMATS-long README.md examples or like the snakemake workflow output. The required files can also be specified manually

Shiny App

Run the app with: Rscript ./run.R

Then the app can be used with a web browser on the same machine that is running the app with the URL http://localhost:8888/. The shiny documentation has more details: https://shiny.posit.co/r/reference/shiny/latest/runapp

With the app open in a browser, plots of the results can be created and viewed

Example

After running the "Isoform Analysis Example" from the main rMATS-long README.md the output under ../example_out/ can be used

• Initially, the Data tab is selected
• Provide the full path to /path/to/example_out/rmats_long/ in the main-directory field
• Click the set-main-directory button
  • Most of the remaining fields in the Data tab should fill in automatically
• Click on the Summary tab
• There are sub-tabs showing
  • A summary pie plot
  • The summary.txt values
  • A table of ASM statistical test results
  • A table of isoform statistical test results
• DDR1 is one significant gene in the output
  • The significant asm_id is 2_0
  • The gene_id is ENSG00000204580.14
• Click on the ASM tab
• Provide 2_0 in the asm-id field
• Click find-gene-id-for-asm to fill in the gene-id field
• There are sub-tabs showing results
• First, scroll down on the Isoform abundance sub-tab and click create plot
  • Creating that plot generates some files needed for the other tabs (like the colors.tsv field at the top of the ASM tab)
• Click on the Isoform structure sub-tab to see additional plots created along with the abundance plot
• Click the Region within gene sub-tab and scroll down and click create plot
• Click the Splicing differences sub-tab and click create table
• Click the Simple splice graph sub-tab and scroll down and click create plot
• Click the Splice graph sub-tab and scroll down and click create plot
  • This plot could take a long time to create for an ASM with a large number of possible splicing paths