iTOL style in gheatmap

[YiweiZhu]

Hi, Prof. Yu,

Is it possible to plot gheatmap in iTOL style? Specifically, the shape of each cell was a circle instead of a square, filling a certain color or leave it blank.

This plot is cited from https://aac.asm.org/content/aac/65/6/e00130-21/F3.large.jpg?width=800&height=600&carousel=1

[xush...@gmail.com]

Yes, It can be generated easily with ggtreeExtra and ggtree. You can refer to the following codes

```

library(ggtree)                                                                                                                                                                                                    library(ggstar)

library(ggtreeExtra)

library(ggplot2)

set.seed(123)

n <- 100

tr <- rtree(n)

dat1 <- data.frame(

           id=rep(tr$tip.label, 8),

           sample=c(rep(c("A1","A2", "A3", "A4"), each=n),

                    rep(c("B1", "B2", "B3", "B4"), each=n)),

           group=c(rep("A", n * 4), rep("B", n * 4)),

           subgroup=rep("T", n*8)

       )

dat1[sample(nrow(dat1), 700), "subgroup"] <- NA

dat1$subgroup <- ifelse(!is.na(dat1$subgroup), dat1$group, NA)

gf1 <- geom_fruit(

           data=dat1,

           geom=geom_star,

           mapping=aes(x=sample, y=id, color=group),

           starshape=15,

           pwidth=0.12

           )

gf2 <- geom_fruit(

           data=dat1,

           geom=geom_star,

           mapping=aes(x=sample, y=id, fill=subgroup),

           starstroke=0,

           starshape = 15,

           pwidth=0.12,

           axis.params = list(axis="x", text.size=1.2, vjust=1, line.size=0)

       )

linecolor <- scale_color_manual(values=c("red", "blue"))

fillcolor <- scale_fill_manual(values=c("red", "blue"), na.translate = FALSE)

fg <- geom_fruit_list(gf2, gf1, linecolor, fillcolor)

p <- ggtree(tr)

p1 <- p + fg + scale_y_continuous(limits=c(-1, NA))

p1

```

[YiweiZhu]

Great! Thank you very much, Shuangbin!

[Yu, Guangchuang]

and to add background colors for tip labels is easy. try the following codes:

x = rtree(30)
d = data.frame(label=x$tip.label, group = sample(letters[1:3], 30, replace=T))
p <- ggtree(x) %<+% d
p + geom_tiplab(geom='label', aes(fill=group), label.size=0)

--
1. G Yu*. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. https://doi.org/10.1002/cpbi.96
2. LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. http://dx.doi.org/10.1093/molbev/msz240
3. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. https://doi.org/10.1093/molbev/msy194
4. G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data, Methods in Ecology and Evolution, 2017, 8(1):28-36. https://doi.org/10.1111/2041-210X.12628
5. Book: https://yulab-smu.top/treedata-book/
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Guangchuang Yu PhD

Professor, Associate director

Department of Bioinformatics
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://yulab-smu.top

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