customizing x axis

[Agnieszka Sitko]

Hi, All, 

is there any pleasant way to customize x axis in ggtree object passed through gheatmap? 

Below is what I am trying to achieve done with grid.arranging two separate ggplot objects (ggtree and heatmap).

I have defined my own formatter:

rootShifter <- function(x, shift) {

    lab <- round(x + as.numeric(shift), 2)

}

and used 

+ scale_x_continuous(label = function(x) { rootShifter(x, shift) })

on ggtree.

And here is my output while scaling gheatmap:

As you may see heatmaps labels were removed from the plot.

Please help me!

Agnieszka

[Yu, Guangchuang]

you need to provide a reproducible example, as I mentioned here, https://guangchuangyu.github.io/2016/07/how-to-bug-author/.

basically, gheatmap is not implemented by grid.arrange which have problem of aligning two ggplot objects like the first figure you showed here.

​

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--

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu, PhD Candidate
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[Agnieszka Sitko]

Hi, Guangchuang Yu,

below you may find my code. Any tips are welcomed.

library(ggplot2)
library(ggtree)
library(dplyr)

# data preparation

txt <- "(C: 2, (A: 1, B:1): 1);"

df <- matrix(rnorm(9), nrow = 3) %>% as.data.frame()

rownames(df) <- c("A", "B", "C")

# an original tree with gheatmap is rooted in zero

((ggtree(read.tree(text = txt)) + geom_tiplab(align = TRUE) +

    theme_tree2()) %>%

    gheatmap(df, offset = 0, width = 0.5, colnames = FALSE)) %>%

    scale_x_ggtree()

Plot without scaling has labels under heatmap but it is also rooted in zero. Let's start shifting. I cannot use both `scale_x_ggtree` and `scale_x_continuous`. So now labels under the heatmap vanish.

rootShifter <- function(x, shift) {

    lab <- round(x + as.numeric(shift), 2)

}

shift <- 2

(ggtree(read.tree(text = txt)) + geom_tiplab(align = TRUE) +

      theme_tree2()) %>%

        gheatmap(df, offset = 0, width = 0.5, colnames = FALSE) +

[Agnieszka Sitko]

And I have just came up with the solution. I am not sure if it's the most gentle one, but I attach it below.

library(ape)

shift <- 2

breaksAndLabelsCalc <- function(tr, shift, gridLength) {

    trHeight <- max(node.depth.edgelength(tr))

    br <- seq(0, trHeight, trHeight / gridLength)

    return(

        list(

            breaks = br,

            labels = as.character(round(br + shift), 2)

        )

    )

}

tree <- read.tree(text = txt)

brLab <- breaksAndLabelsCalc(tree, shift, 6)

((ggtree(tree) + geom_tiplab(align = TRUE) +

    theme_tree2()) %>%

    gheatmap(df, offset = 0, width = 0.5, colnames = FALSE)) %>%

    scale_x_ggtree(breaks = brLab$breaks, labels = brLab$labels)

[Yu, Guangchuang]

p = ggtree(read.tree(text = txt)) + geom_tiplab(align = TRUE) + theme_tree2()
p$data$x = p$data$x +2
p %>%
    gheatmap(df, offset = 0, width = 0.5, colnames = FALSE) %>%
    scale_x_ggtree()

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[Agnieszka Sitko]

Oh, thank you. That is so much easier!

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