pathview-internal: Internal functions

In pathview: a tool set for pathway based data integration and visualization

Description

Not intended to be called by the users.

Details

These functions are not to be called by the user directly.

Functions parseReaction2, parseKGML2, KEGGpathway2Graph2 and parseKGML2Graph2 parse KEGG pathways from KGML files. Function subtypeDisplay.kedge and data KEGGEdgeSubtype extact and store edge subtypes and corresponding rendering information. All these functions/data were modified from the original copies in KEGGgraph package.

Function kegg.legend generates legend for KEGG edge and node types. Function pathview.stamp generates pathview sisgnature on graphs.

Function colorpanel2 comes from gplots package function colorpanel.

Functions max.abs and random among others are method to summarize data at molecular level or node level when multiple items mapping to the same ID/node.

Function circles, ellipses and sliced.shapes draw KEGG nodes in colored shapes (circles and ellipses).

Functions deComp and rownorm were written by Weijun Luo, the author of gage package.

pathview documentation built on Dec. 12, 2020, 2 a.m.