Dash Bio vs R packages features comparison about dash-bio HOT 8 CLOSED

Here is the order in which I intend to compare the R/python apps:

1. MSA viewer
2. 3d molecule viewer/Speck
3. Needleplt
4. Cytoscape
5. Clustergram
6. Circos
7. Phylocanvas
   I can check the rest of the apps once done with the ones above :)

from dash-bio.

• In my case, it's more phylogenetic and clustering tools:

1. Phylogenetic tools

• ggtree
• Phylocanvas
• phangorn
• phytools
• ctv

2. Clustering tools

• pvclust
• mclust
• fpc
• Clustergram

Some of them was cited by nchtra, I'll add more after :-)

from dash-bio.

@nchtra @NadiaTahiri

I looked at a couple differences between Dash Circos and R Circos. I wrote up some feature requests for the library that Dash Circos is wrapping: plotly/react-circosJS#7

from dash-bio.

Some options to add for CLUSTERGRAM (based on https://cran.r-project.org/web/packages/heatmaply/vignettes/heatmaply.html):

• Different color palettes to include the various color scales including grey scale
• Data transformation including scaling, Normalization and percentage scales
• identifying and displaying missing data (NaN)
• Customization of branch colors of dendrograms
• Option to display row/column labels

from dash-bio.

3D molecule viewer:

• Rainbow color scheme for displaying the chains
• Color molecule by secondary structure potentially using information from the header section of the PDB file
• Display selected atoms with distinct colors and representation (stick, cartoon etc)
• For multi-model PDB structures (with multiple strucures within a PDB file corresponding to these 'models'), display individual models with a corresponding dropdown for selecting different models
• Hide/unhide water molecules
• Surface representation for molecules like this: https://www.rcsb.org/3d-view/3AID/1. Note that this feature is not present in the react version of molecule3d and hence may not be possible to add at the moment in the dash app
• Ligand viewer - Display stick representation of ligand molecules and amino acid residues of protein that are within a minimum distance from the ligand

from dash-bio.

Sequence alignment viewer:

• Choice of different color schemes for amino acids based on their chemical properties would be great
• adding a weblogo-like output for the alignments - https://weblogo.berkeley.edu/examples.html

from dash-bio.

Phylocanvas viewer:

• tree visualization via treetype (i.e. rectangular, circular, hierarchical, diagonal and radial)
• modification of size: (textsize, nodesize, linewith)
• customize labels: showlabels, alignlabels
• customize figure: showhistory, showcontextmenu, showscalebar
• adding HTMLWidget : width, height and elementId

from dash-bio.

Heatmaply viewer:

• customize Figure: scale, margins, and
• column: ColSideColors, cexCol, labCol
• row: cexRow, RowSideColors, labRow
• legend: main, xlab, ylab

from dash-bio.