Visualization

Run It

It is possible to visualize all kind of predictions using the shipped Dashboard

Therefore simply type:

RNAdist visualize --input path/to/pediction/file.pckl --fasta path/to/fasta

This will run the dash server using the default port and ip address. You can now use the application if you open your browser and type http://127.0.0.1:8080/ into the url bar. The tool supports multiple prediction files.

Note

The tool supports multiple prediction files. Just put multiple whitespace-separated paths after the --input flag.

Warning

The predictions must originate from the same fasta file. Else the Dashboard will crash.

Note

The --fasta flag is optional but it will include additional information about nucleotides during visualization

RNAdist Visualizer

Now that you started the visualization. It is time to talk about what you see here. In the bottom right you can find the selector pane [2]. Here you can select the Fasta header of the sequence you want to inspect.

Note

The Dropdown Menu is restricted to 100 entries. If your prediction file has more sequences, start typing the name of the sequence you search for and it will show up.

Via the Nucleotide Index input you can specify for which nucleotide expected distances should be shown in the upper distance graph [1].

Last but not least there is a heatmap [3] in the lower left corner showing distances for all nucleotide combinations. You can download this heatmap as a tsv file using the Export Heatmap to TSV Button in the Selector Pane.