Closed sridhar0605 closed 3 months ago
This is a problem with graphviz library most likely, the resulting graph is too big for it to generate a PNG out of it. I believe that it is the graphviz library has trouble dealing rendering an overly large graph,
Set the mincount to 2 instead of 1 and you will get an output but it is 13MB image,
The mincount is the parameter that has the strongest effect. The mincount represents the minimum number of genes share that function. Usually filtering above 1 reduces the graph size quite a bit.
Thus, it is not the number of genes one includes but the threshold via the mincount that determines the limitations relative to a gene list.
Maybe I could call that parameter something else, that better indicates what it does.
I'll add a clear note in the README about the effect of mincount
This is not fixable in the sense that it is a limitation of the graph rendering engine,
there is no limit on the number of genes that can be annotated for example, large lists can also be reduced in size
but depending on which front end one uses the engine may not be able to draw a PNG when it can still make an SVG for example.
in version 0.9.4., the main web interface has documentation that talks about reducing graph sizes.
When I use dummy gene list below with default params (All roots) Having a hard time saving the plot, Am i missing something?
I tried setting BP, MF, CC roots individually too, hoping that this would reduce plotting space but that did not seem to help.