Phylo Explorer

Introduction

This app can be used for quick retreival of NCBI taxon information with detailed and formated output. A quick visualization of hierarchical data (whether NCBI retrieved or provided) using multiple tree view

This shiny apps uses: taxize: for NCBI querying tool. d3treeR, treemap, sunburstR, d3Tree, D3partitionR: for all kinds of treeview plot. DT, data.table: to table manipulation and display. colourpicker: for color picking. shinyBS: for progressing status.

Gallery

Accepted inputs

1 ) Hierarchical structure data

If you already have a hierarchical structured data with intensity infomration(see the sample data, intensity as last column), you can directly plot from the data provided. This module will use the intensity value to indicate the relative expression/proportion on the plot.

2 ) Taxon Id list

In the taxon id list mode, users can simply paste a taxon ID list to start. The application will retrieve detailed taxon information from NCBI from NCBI using the taxon ids provided. Further plots can be made from the retrieved data.

3 ) Taxon Id and abundance

In the taxon id list mode, users can simply upload a table with two columns: one with taxon ids, the second one is expression/abudnace. The application will retrieve detailed taxon information from NCBI using the taxon ids provided. Further plots can be made from the retrieved data. This module will use the abundance value to indicate the relative expression/proportion on the plot. The application will retrieve detailed taxon information from NCBI.


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