Tree with barplot

[o.willi...@gmail.com]

Hello, 

I have been following the manual in order to plot tree with a bar graph alongside.

I can use the facet plot method but ideally I would like to change the relative widths of the plot. 

So I am using the method with aplot outlined here http://yulab-smu.top/treedata-book/chapter7.html in the section for composite plots.

Is there a method to plot only the tree and the barplot side by side, without the heatmap in the middle? I have attached an image of what I am aiming for.

I found a workaround, by adding a blank dummy plot in between. See the code below. However, I was wondering if there was a simpler way of doing this? 

library(ggplot2)

library(ggtree)

library(cowplot)

library(aplot)

set.seed(2019-10-31)

tr <- rtree(10)

# dataset 1

d1 <- data.frame(

  # only some labels match

  label = c(tr$tip.label[sample(5, 5)], "A"),

  value = sample(1:6, 6))

# dataset 2

d2 <- data.frame(

  label = rep(tr$tip.label, 5),

  category = rep(LETTERS[1:5], each=10),

  value = rnorm(50, 0, 3)) 

# tree

g <- ggtree(tr) + geom_tiplab(align=TRUE)

# plot 1

p1 <- ggplot(d1, aes(label, value)) + geom_col(aes(fill=label)) + 

  geom_text(aes(label=label, y= value+.1)) +

  coord_flip() + theme_tree2() + theme(legend.position='none')

# plot 2

p2 <- ggplot(d2, aes(x=category, y=label)) + 

  geom_tile(aes(fill=value)) + scale_fill_viridis_c() + 

  theme_tree2() 

# plot side by side

p2 %>% insert_left(g) %>% insert_right(p1, width=.5) 

# nether work as intended 

g %>% insert_right(p1)

p1 %>% insert_left(g)

# create dummy data to sit in between

d2_dummy <- data.frame(label = tr$tip.label,

                       category = LETTERS[1:5]) 

# dummy plot

p2_dummy <- ggplot(data = d2, aes(x=category, y=label)) + theme_void()

# plot side by side with dummy plot in between

p2_dummy %>% insert_left(g, width = 10) %>% insert_right(p1, width=5) 

Best wishes

Ollie

 

[Yu, Guangchuang]

nice hack.

IMO, facet_plot is very better for this case. If you wan to adjust facet width, there is a facet_widths() function provided in ggtree and was presented in the following paper:

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

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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://guangchuangyu.github.io

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[o.willi...@gmail.com]

Hello, 

Thank very much for pointing out the facet_widths function, it is just what I needed, and apologies I hadn't spotted it beforehand

Best wishes

Ollie