Open PSSchacksen opened 2 years ago
Not sure why, but gheatmap cuts the top row and last column in my combined tree and heatmap
`primer_nosZ <- ape::read.tree('data/nosZ_comb_qiime-vsearch_MGP1000-ref_muscle-1.faa.contree')
primer_nosZ_meta_intervals_grey <- read.csv('data/Primer_metadata_intervals_grey.csv')
rownames(primer_nosZ_meta_intervals_grey) <- primer_nosZ_meta_intervals_grey$ID
primer_nosZ_meta_intervals_grey2 <- subset(primer_nosZ_meta_intervals_grey, select = -c(ID, Genus, Family, Order, Class, Phylum, clade, 43:59))
primer_nosZ_tree <- ggtree(primer_nosZ) + geom_treescale(x = 0, y = -1.3, fontsize = 4, offset = 0.5)
primer_nosZ_tree_view <- primer_nosZ_tree%<+%primer_nosZ_meta_intervals_grey + geom_text(aes(label=Genus), size = 3, hjust = -0.1) primer_nosZ_tree_view
primer_nosZ_heatmap <- gheatmap(primer_nosZ_tree_view, primer_nosZ_meta_intervals_grey2, font.size = 2.5, width = 1.3, colnames_angle = 90, color='black', offset = 0.5, hjust = 0.95, colnames_offset_y = -0.3) + scale_x_ggtree() + scale_y_continuous(expand = c(0.04, 3)) + scale_fill_manual(values=c("0" = "white", "1-10" = "gray75", "10-1000" = "gray40", "1000+" = "black")) + theme(legend.position="none") + xlim(0, 6.5) + ylim(-4, 40) primer_nosZ_heatmap `
Primer_metadata_intervals_grey.csv nosZ_comb_qiime-vsearch_MGP1000-ref_muscle.fa.zip
Not sure why, but gheatmap cuts the top row and last column in my combined tree and heatmap
`primer_nosZ <- ape::read.tree('data/nosZ_comb_qiime-vsearch_MGP1000-ref_muscle-1.faa.contree')
primer_nosZ_meta_intervals_grey <- read.csv('data/Primer_metadata_intervals_grey.csv')
rownames(primer_nosZ_meta_intervals_grey) <- primer_nosZ_meta_intervals_grey$ID
primer_nosZ_meta_intervals_grey2 <- subset(primer_nosZ_meta_intervals_grey, select = -c(ID, Genus, Family, Order, Class, Phylum, clade, 43:59))
primer_nosZ_tree <- ggtree(primer_nosZ) + geom_treescale(x = 0, y = -1.3, fontsize = 4, offset = 0.5)
primer_nosZ_tree_view <- primer_nosZ_tree%<+%primer_nosZ_meta_intervals_grey + geom_text(aes(label=Genus), size = 3, hjust = -0.1) primer_nosZ_tree_view
primer_nosZ_heatmap <- gheatmap(primer_nosZ_tree_view, primer_nosZ_meta_intervals_grey2, font.size = 2.5, width = 1.3, colnames_angle = 90, color='black', offset = 0.5, hjust = 0.95, colnames_offset_y = -0.3) + scale_x_ggtree() + scale_y_continuous(expand = c(0.04, 3)) + scale_fill_manual(values=c("0" = "white", "1-10" = "gray75", "10-1000" = "gray40", "1000+" = "black")) + theme(legend.position="none") + xlim(0, 6.5) + ylim(-4, 40) primer_nosZ_heatmap `