eliminating overlap of outer bar plots and inner heat maps

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Tiago Pereira

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Feb 13, 2024, 9:46:29 AMFeb 13

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Hi everyone

I have used the code for the circular tree with additional data annotation (Fig. 10.2, https://yulab-smu.top/treedata-book/chapter10.html) but I am having issues with the overlap of the inner heatmap rings and the outer bartplots. See figure attached.

I have played with the different parameters in the code (also attached), but so far I have not been successful to either (1) reduce the size of the inner heatmap rings (I have only two categories) or (2) move the barplots further out, so they do not overlap.

I am wondering if you can give me some guidance with this issue.

Thanks in advance!

`tree_nema_18S <- read.tree("data/wofa-asv-nematodes-rep-sequences.tree")
dat1_nema <- read.csv("exported_tables/combined/wofa_nematode_ludox_tippoint_attr.csv")
dat2_nema <- read.csv("exported_tables/combined/wofa_nematode_ludox_ringheatmap_attr.csv")
dat3_nema <- read.csv("exported_tables/combined/wofa_nematode_ludox_barplot_attr.csv")

dat2_nema$Group <- factor(dat2_nema$Group,
levels=c("Gp1", "Gp2"))

dat3_nema$Group <- factor(dat3_nema$Group,
levels=c("Gp1", "Gp2"))

p_nematoda <- ggtree(tree_nema_18S, layout="fan", size=0.15, open.angle=5)
p_nematoda

p_nematoda <- p_nematoda %<+% dat1_nema + geom_fruit(geom=geom_star,
mapping=aes(fill=Family, size=Size),
position="identity",starstroke=0.1)+
scale_fill_manual(values=c("#FFC125","#87CEFA","#7B68EE","#808080","#EE6A50",
"#9ACD32","#D15FEE","#FFC0CB","#800080","#8DEEEE",
"#006400","#800000","#f58231","#191970","#9a6324",
"#46f0f0","#1F78B4","#bcf60c","#e6beff","#4363d8",
"#008080","#e6194b","#f032e6","#aaffc3", "lightgreen",
"#ffe119","#75","#fffac8","#9a6324","#FB9A99",
"#33A02C","#fabebe","#6A3D9A", "gray", "lightblue", "darkblue", "mediumspringgreen"),
guide=guide_legend(keywidth = 0.5, keyheight = 0.5, order=1,
override.aes=list(starshape=15)),
na.translate=FALSE)+
scale_starshape_manual(values=c(15, 1, 3, 5, 7, 2, 10, 9),
guide=guide_legend(keywidth = 0.5, keyheight = 0.5, order=2),
na.translate=FALSE)+
scale_size_continuous(range = c(1, 2.5),
guide = guide_legend(keywidth = 0.5, keyheight = 0.5, order=3,
override.aes=list(starshape=15)))+
new_scale_fill()+
geom_fruit(data=dat2_nema, geom=geom_tile,
mapping=aes(y=ID, x=Group, alpha=Abundance, fill=Group),
color = "grey50", offset = 0.04, size = 0.02)+
scale_alpha_continuous(range=c(0, 1),
guide=guide_legend(keywidth = 0.3, keyheight = 0.3, order=5)) +
geom_fruit(data=dat3_nema, geom=geom_bar,
mapping=aes(y=ID, x=HigherAbundance, fill=Group),
pwidth=0.38, orientation="y", stat="identity")+
scale_fill_manual(values=c("#75", "#46f0f0"),
guide=guide_legend(keywidth = 0.3, keyheight = 0.3, order=4))+
geom_treescale(fontsize=1.2, linesize=0.3, x=0.1, y=0.0001) +
theme(legend.position=c(1.2, 0.5),
legend.background=element_rect(fill=NA),
legend.title=element_text(size=5),
legend.text=element_text(size=4),
legend.spacing.y = unit(0.02, "cm"))
p_nematoda