pathwayanalysisplatform / proteoformnetworks Goto Github PK

Implement calculation of network overlapping scores to compare the overlaps at gene and proteoform level

• Implement with tests calculation of disease module overlaps at gene level

• Create disease modules in Python
• Create disease modules in C++
• Test that some modules are the same in both procedures

• Plot a pathway with the 3 types of construction methods
• Test 3 pathways were constructed correctly
• Get list of all pathways
• Get number and list of articulation points and bridges
• Violin plot for the numbers of each pathway
• Plot a pathway highlighting the articulation points and bridges
• Modify the violin plots to Normalize by size the number of articulation points and bridges with respect to the total number of vertices and edges in the graph
• Select 3 pathways where the numbers change and plot them
• Modify pathway plots to show controls of bokeh to zoom in

• Calculate difference of scores between gene and proteoform level using all scores.
• Plot distribution of each score difference

After the conversion of the gene network to proteoform network, implement with tests the calculation of the disease modules.

Plot simple overlap by nodes at gene level.

Implement and test the conversion of gene disease modules to proteoform modules.

• Add documentation comments for the most important functions