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.

Try the sample data for a quick demo

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.

Try the sample data for a quick demo

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.

Try the sample data for a quick demo

Data preparation

Copy paste a taxon id list
Try the sample data for quick evaluation

Data preparation

File format has to be tsv or csv
Try the sample data for correct file format, before and uploading

Upload data file (tsv/csv)

Table uploaded

NCBI retrieved

Data preparation

File format has to be tsv or csv
Try the sample data for correct file format, before and uploading

Upload data file (tsv/csv)

Table uploaded

Querying NCBI, please wait ...

Loading, please wait ...

Loading, please wait ...

Loading, please wait ...

About

This apps 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

Acknowledgement

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.

Contact

Author: Zhibin Ning
Email: ningzhibin@gmail.com
Suggestions and bug report

Change log

V0.2: 20190903, bug fix, NCNI linits the api access, use API key instead; pdf(NULL) fix the cannot open file 'Rplots.pdf' error
V0.1: 20171211, app online

Error Log (for debugging)