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-   -   GOplot GOcluster plots (http://seqanswers.com/forums/showthread.php?t=88972)

polaxgr 04-25-2019 01:00 AM

GOplot GOcluster plots
 
Hello all. I ve been trying to do some plots from GOplots in R. But i have some issues regarding GOcluster GOheat and GOVenn. With GOcluster (myprocess file is names of GO):

GOCluster(circ, myProcess, clust.by = 'logFC', term.width = 2)

i get an error

Error in stats::hclust(distance, method = clust) : NA/NaN/Inf in foreign function call (arg 11).

I have searched a bit online and i guess the problem is that i got NA's values and Inf in my circ data ( circ <- circle_dat(david, genelist). After inspecting my circ data, I have NA's and Inf values. So my question is what do i do so i can complete the plot ? Remove somehow the NA's / Inf values or add an option to overlook them ? I would prefer the 2nd option, if there is.

EDIT: after removing Inf values from my genes and then doing david ontology it worked.

And about GOheat, its much simpler i think. I cant get the names of the genes on the heatmap.

GOHeat(chord[,-7], nlfc = 0)

About GOVenn when trying to run :

l1 <- subset(circ, term == 'activation of MAPK activity', c(h06_specific_noinf,logFC))

i get an error : Error in x[j] : invalid subscript type 'list'

Thanks!


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