I am building heatmaps from the MRfulltable outputs obtained in metagenomeseq. When preparing the heatmap I am able to filter OTUs by adjusted p-value, so I can prepare a heatmap chossing only the ssignificant OTUs, however it would be also desirable to remove those significant OTUs with low count numbers.... When I try to use a similar code, lets say
"significant_OTU <- which(MRfulltable(Donor_A, number=length(Donor_A$taxa))"$countsingroup1>100"
I get an error,
I paste my code below, thanks in advance for the response and also for your time.
heatmapColColors = c("grey","green")[as.integer(factor(pd_Donor$Donor))]
heatmapCols = colorRampPalette(c("white","light blue","blue","dark blue"))(50)
significant_OTU <- which(MRfulltable(Donor_A, number=length(Donor_A$taxa))$adjPvalues<=0.05)
plotMRheatmap(obj = metHMEX6_A[significant_OTU,] , n=length(significant_OTU), margins=c(4,14),cexRow = 0.7, cexCol = 1, trace = "none", col = heatmapCols, ColSideColors = heatmapColColors, lhei = c(2, 8))