Shiny is a powerful and open source interactive data visualization Web Framework based on the R language. It was developed by the RStudio company, and the source code can be downloaded in GitHub repo.
The followed R command
install.packages('shiny') can be used to install it. Several useful articles about shiny can be found in here
In general, it is best choices of annovarR for in-house web service for genetic variants data annotation and visulization. We hope this shiny application can improve the interactivity of annovarR, and reduce its use difficulty for unprofessional. Meanwhile, we also provides a set of functions to build the simple cloud computing app for other purpose, such as variant calling, RNA-seq data analysis, etc.
Opencpu is a tool for R users to build the web service REST API. It is a good choice for those command line users to finish specific R tasks without the Rstudio GUI or web graphic interface.
A simple API document can be found in here. annovarR will use the related API to provide the REST API.
When you started a instance of annovarR shiny app in Rstudio or R client, it will shows the URL and port:
Listening on http://127.0.0.1:3234. The port was random, and you can control the host and port of annovarR by parameteres
annovarR README.md was include as the introducation page. Total nine tab item were provided:
Dashbord page mainly shows the monitor of system, such as disk and memory, and tasks. Output of
Sys.getenv() also were provided.
Annotation page is the main interface for genetic variants annotation. It will submit a annotation work to the worker pool, and you can get the output figures/tables or other format files via input a post key in the
Visulization page is the main interface for genetic variants visulization. It will generated the interactive plots or tables in the output boxes. Not like annotation tab item, all tools in the visulization will returned the real time calculation results according to the users inputs.
Progress bar indicator will shows in the right-bottom of page, and other warning or error message were also print in the page region.
The followed figure is the demo output of function oncoprint of maftools, a bioconductor package for visulization of MAF format files.
We provides the
pipeline page for another purpose bioinformatics analysis. CEMiTool, a gene co-expression analysis bioconductor package, was used to as the example of this page. It will generate the
File Viewer page is a integrated view page for uploaded files. Now, only the text format files were supported to render the content by
DT package. Besides, you can also to download and delete related files via click respectively rows
Rendered table content:
Need confirmed delete action:
Upload page provided the upload function that will be used as the input for annotation and visulization tools.
This page mainly to provide the functions for download of annotation database. We will support more download functions in the future, such as raw sequencing data or other gene expression data. It also will submit a task to worker pool, and you can get the post key to see the related log of download process.