ggplot2 generate same plot for different variables in a for loop

Question

I am trying to loop through a list containing numbers only. For each loop, I convert the column from char to numeric, and then I attempt to plot it. A basic example of my code is:

library(ggtree) 
library(treeio)
library(tidyverse)
library(ggnewscale)
library(ggtreeExtra)
library(argparse)
library(RColorBrewer)
library(rlist)
library(stringr)

tree <- read.tree("/...") #PLEASE REPLACE THIS WITH THE LOCATION TO 'tree_newick.nwk'

tipcategories = read.csv("....", # PLEASE REPLACE THIS WITH THE LOCATION TO 'plot.tsv'
                     sep = " ",
                     header = TRUE,
                     stringsAsFactors = FALSE)

dd = as.data.frame(tipcategories)

p <- ggtree(tree) + ylim(-1, NA) + theme_tree2() 

p <- p %<+% dd + geom_tiplab(size=1)   

n <- 60
qual_col_pals = brewer.pal.info[brewer.pal.info$category == 'qual',]
col_vector = unlist(mapply(brewer.pal, qual_col_pals$maxcolors, 
rownames(qual_col_pals)))

columns = c("Column1", "Column2")

for (col in columns) {

  p <- p + new_scale_fill()

  dd[[col]] <- as.numeric(as.character(dd[[col]]))

  p <- p + geom_fruit(geom=geom_tile, mapping=aes(fill=dd[[col]]), width=2, offset=0.05) +
    scale_fill_continuous(name=col, low='blue', high='red')

}

p <- p + theme(legend.text = element_text(size = 5), legend.key.size = unit(0.3, 'cm'))

ggsave("....") # PLEASE REPLACE THIS WITH WHERE YOU WANT TO SAVE IT

The tree data is (please put in file and replace filename with dots in read tree):

(((((((A:4,B:4):6,C:5):8,D:6):3,E:21):10,((F:4,G:12):14,H:8):13):13,((I:5,J:2):30,(K:11,L:11):2):17):4,M:56);

The metadata file (please put in file and replace filename with dots in read.csv):

Accession1 Column1 Column2   
A 10 130
B 20 120
C 30 110 
D 40 100
E 50 90
F 60 80 
G 70 70
H 80 60
I 90 50
J 100 40
K 110 30
L 120 20
M 130 10

The above works fine for just one columns, however, when trying to plot 2 columns, the second column always overwrites the first column, and the first column ends up looking exactly the same as the second column. The below image shows the result of running the program normally.

The first column (column1) is actually supposed to look like this:

Could anyone provide help as to how to fix this?

Answer 1

It really take a lot of time to reproduce your case as you have so many packages that I didn't use :)

Explaination of the issue: ggplot does not render any graph at the time you call the geom and passing data and mapping aes. ggplot just store the name reference to the data variable. Only when render it actually get the value and plot. In your case, you are passing reference dd[[col]] and as col change value through for loop while ggplot always reference to col so it ended render two bar of the same data of the last column value is Column2. You can verify this by changing order of the column and put Column1 at last then you will see two bar of Column1 instead.

Solution: create unique reference for each loop

Initial setup with data in dput format

library(ggtree)
library(treeio)
library(tidyverse)
library(ggnewscale)
library(ggtreeExtra)
library(argparse)
library(RColorBrewer)
library(rlist)
library(stringr)

tree <- structure(list(edge = structure(c(14L, 15L, 16L, 17L, 18L, 19L, 
  20L, 20L, 19L, 18L, 17L, 16L, 21L, 22L, 22L, 21L, 15L, 23L, 24L, 
  24L, 23L, 25L, 25L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 1L, 2L, 
  3L, 4L, 5L, 21L, 22L, 6L, 7L, 8L, 23L, 24L, 9L, 10L, 25L, 11L, 
  12L, 13L), .Dim = c(24L, 2L)), edge.length = c(4, 13, 10, 3, 
    8, 6, 4, 4, 5, 6, 21, 13, 14, 4, 12, 8, 17, 30, 5, 2, 2, 11, 
    11, 56), Nnode = 12L, tip.label = c("A", "B", "C", "D", "E", 
      "F", "G", "H", "I", "J", "K", "L", "M")), class = "phylo",
  order = "cladewise")

tipcategories <- structure(
  list(Accession1 = c("A", "B", "C", "D", "E", "F", "G", 
    "H", "I", "J", "K", "L", "M"), Column1 = c(10L, 20L, 30L, 40L, 
      50L, 60L, 70L, 80L, 90L, 100L, 110L, 120L, 130L), Column2 = c(130L, 
        120L, 110L, 100L, 90L, 80L, 70L, 60L, 50L, 40L, 30L, 20L, 10L
      ), X = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA), 
    X.1 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA
    ), X.2 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
      NA)), class = "data.frame", row.names = c(NA, -13L))

Your code with plot generation and modification to avoid using same variable for the plot which cause the issue you got in OP

dd <- as.data.frame(tipcategories)

p <- ggtree(tree) + ylim(-1, NA) + theme_tree2()

p <- p %<+% dd + geom_tiplab(size = 1)

n <- 60
qual_col_pals <- brewer.pal.info[brewer.pal.info$category == "qual", ]
col_vector <- unlist(mapply(
  brewer.pal, qual_col_pals$maxcolors,
  rownames(qual_col_pals)
))

columns <- c("Column1", "Column2")

for (col in columns) {
  p <- p + new_scale_fill()

  # assign the value of dd[[col]] into a new variable using the name column
  assign(col, as.numeric(as.character(dd[[col]])))
  
  # using bang bang (!!) & sym to reference the variable inside ggplot call
  # this allow the ggplot to reference to different variable when finally render
  # plot at the end
  p <- p + geom_fruit(geom = geom_tile, mapping = aes(fill = !!sym(col)),
    width = 2, offset = 0.05) +
    scale_fill_continuous(name = col, low = "blue", high = "red")
}

p <- p + theme(legend.text = element_text(size = 5),
  legend.key.size = unit(0.3, "cm"))

p

^{Created on 2021-04-15 by the reprex package (v2.0.0)}