PathVisio / pathvisio

PathVisio - pathway editor, visualization and analysis software
http://www.pathvisio.org
Apache License 2.0
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total element count does not seem to exclude duplicates #35

Open mkutmon opened 7 years ago

mkutmon commented 7 years ago

Reported by Lars: The attached screenshot shows that PathVisio does not seem to take into account duplicate items when it computes the total number of elements on the pathway.

The number of items on this (old) version of the Cholesterol Biosynthesis pathway is 33, but one is a duplicate (FDPS, bottom lower corner - both boxes are properly annotated with NCBI gene ID 2224). So the total should be 32, not 33. At least, when the intention is to count the number of unique elements, which I expected.

When considering the measured (n) column, PathVisio does correctly count 17 (the 18 boxes with data again include the pair of duplicates).

mkutmon commented 7 years ago

image

DeniseSl22 commented 5 years ago

So, this should count two DataNodes as 1, when they have been annotated with the same identifier right? Otherwise we will get into the mess of ID mapping, and it becomes very confusing to calculate this.... I'll add it on the list for PV4 (if it hasn't been fixed already).