I am comparing the microbiome generated from MiSeq and PacBio at different taxonomic levels using VennDiagram.
I already extracted taxa at each taxonomic level from each technology as columns (MiSeq, PacBio) and created excel sheets for each level to draw venndiagrams of intersections.
For example, at the phylum level, I used this code:
ven <- venn.diagram( x = list(miseq_vector, pacbio_vector), col=c("#0000FF", '#00FF00'), category.names = c("MiSeq" , "PacBio " ), fill = c(alpha("#0000FF",0.5), alpha('#00FF00',0.5)), main ="Phylum level", main.fontface = "bold", main.fonfamily = "serif", main.cex = 3, main.just = c(0.5, 1), fontfamily = "serif", fontface = "bold", lwd = c(1,1), cat.cex = c(2,2) , cex= c(1,1,1), cat.col = c("black", "black"),compression = "lzw", filename="#pollen_phylum.tiff", output=TRUE, cat.pos = c(0, 30)) ven
The figure is generated as below,
However, number of phyla for miseq is 20 and for pacbio is 8. The count is correct for miseq and the intersection, but I have an additional value for pacbio. I tried using zeros and the word “NotAvailable” for empty cells in pacbio columns since I am comparing 2 vectors of the same length, and in both cases, these values were counted as a field (as shown in the figure 2 taxa for pacbio only, however, it is only one). I do not know how to compare 2 vectors of different lengths without using zeros or NA since each is counted as a value. I need to match both columns and draw venndiagram.