For loop to create a list of ggplots always save the same coordinates for points and segments

Question

first you need to load these packages:

library(ggplot2)
library(ggrepel)

I have a dataframe "dframe" like this:

V1          V2           V3          V4          V5          V6          V7          Groups
0.05579838 -0.44781204 -0.164612982 -0.05362210 -0.23103516 -0.04923499 -0.06634579      1
0.14097924 -0.35582736  0.385218841  0.18004788 -0.18429327  0.29398646  0.69460669      2
0.10699838 -0.38486299 -0.107284020  0.16468591  0.48678593 -0.70776085  0.20721932      3
0.22720072 -0.30860464 -0.197930310 -0.24322096 -0.30969028 -0.04460600 -0.08420536      4
0.24872635 -0.23415141  0.410406163  0.07072146 -0.09302970  0.01662256 -0.21683816      5
0.24023670 -0.27807097 -0.096301697 -0.02373198  0.28474825  0.27397862 -0.29397324      6
0.30358363  0.05630646 -0.115190308 -0.51532428 -0.08516130 -0.08785924  0.12178198      7
0.28680386  0.07609196  0.488432908 -0.13082951  0.00439161 -0.17572986 -0.25854047      8
0.30084361  0.06323714 -0.008347161 -0.26762137  0.40739524  0.22959024  0.19107494      9
0.27955675  0.22533959 -0.095640072 -0.27988676 -0.04921808 -0.10662521  0.19934074     10
0.25209125  0.22723231  0.408770841  0.13013867 -0.03850484 -0.23924023 -0.16744745     11
0.29377963  0.13650247 -0.105720288 -0.00316556  0.29653723  0.25568169  0.06087608     12
0.24561895  0.28729625 -0.167402464  0.24251060 -0.22199262 -0.17182828  0.16363196     13
0.25150342  0.25298115 -0.147945172  0.43827820  0.02938933  0.01778563  0.15241257     14
0.30902922 -0.01299330 -0.261085058  0.13509982 -0.40967529 -0.11366113 -0.06020937     15
0.28696274 -0.12896680 -0.196764195  0.39259942  0.08362863  0.25464125 -0.29386260     16

Here is a reproducible dataframe that you can use from Mark Peterson:

dframe <-
  rnorm(70) %>%
  matrix(nrow = 10) %>%
  as_tibble() %>%
  setNames(paste0("V", 1:ncol(.))) %>%
  mutate(Groups = 1:nrow(.)
         , Label = 1:nrow(.))

I created a table of combinations of columns I want to be used from my dataframe:

#Create all possible combinations
combs<-expand.grid(seq(7),seq(7))
#Remove duplicate and order
combs<-combs[combs$Var1 != combs$Var2,]
combs<-combs[order(combs[,1]),]

then I made a for loop supposed to generate a list of ggplots, 1 plot by combination:

list_EVplots<-list()
  for(i in seq(nrow(combs))){
    list_EVplots[[paste(combs[i,1],"&",combs[i,2])]]<- ggplot(data=dframe) +
      ggtitle(paste("Eigenvector Plot - Pairwise",
                    "correlation with","adjustment")) +
      geom_point(aes(x = dframe[,combs[i,1]], y = dframe[,combs[i,2]],
                     color = Groups)) +
      geom_segment(aes(x = rep(0,nrow(dframe)), y = rep(0,nrow(dframe)),
                       xend = dframe[,combs[i,1]], yend = dframe[,combs[i,2]],
                       color = Groups),
                   size = 1, arrow = arrow(length = unit(0.3,"cm"))) +
      geom_label_repel(aes(x = dframe[,combs[i,1]], y = dframe[,combs[i,2]],
                           label = rownames(dframe))) +
      scale_color_manual(values=colors) +
      xlab(paste0("Eigenvector ",combs[i,1])) +
      ylab(paste0("Eigenvector ",combs[i,2])) +
      theme(plot.title = element_text(hjust = 0.5),
            axis.title = element_text(size = 13),
            legend.text = element_text(size=12)) +
      geom_hline(yintercept = 0, linetype="dashed") +
      geom_vline(xintercept = 0, linetype="dashed")
  }

After running this for loop, I obtain my list "list_EVplots". Problem: iterations seem to work for xlab() and ylab(), it also work for the names of plots in the list, but the coordinates of geom_point(aes()) and geom_segment(aes()) do not change. Coordinates stay the same when they obviously should change! I think the coordinates stay locked on the one used for the first plot of the first iteration. If anyone has the solution for that I would be very grateful for your help.

Working under Linux 16.04 with R Studio. R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"

I tried with a subsetted dataframe with only the columns I wanted to work with instead of using an 8 columns dataframe: didn't work.

Expected: The list should contain different plots: all plots should be different.

Problem: All plots have the same coordinates for dots and segments in the list.

Answer 1

The simplest answer is often the easiest one: try to avoid using for loops in places where lapply is more appropriate. I don't see anything obvious in your code that suggests where the problem lies, but I am guessing that it is a problem in the deeply nested [] statements.

Here is an approach using lapply and aes_string to handle the variables. If you want something other than a full pairwise set of plots, you may have to modify the calls to the two lapply's a bit.

First, some reproducible data (made using dplyr). Note that I made the Labels explicit instead of relying on the rownames (this is good practice, and far easier to use in calls to ggplot).

dframe <-
  rnorm(70) %>%
  matrix(nrow = 10) %>%
  as_tibble() %>%
  setNames(paste0("V", 1:ncol(.))) %>%
  mutate(Groups = 1:nrow(.)
         , Label = 1:nrow(.))

Then, I am pulling out the columns that you want to use for your plots. I am naming them so that the returned list has the column names automatically assigned.

my_cols <-
  names(dframe)[1:7] %>%
  setNames(.,.)

Then, just set up a nested lapply to work through all of the pairwise comparisons:

plot_list <-
  lapply(my_cols, function(col1){
    lapply(my_cols, function(col2){

      if(col1 == col2){
        return(NULL)
      }

      ggplot(dframe) +
        ggtitle(paste("Eigenvector Plot - Pairwise",
                      "correlation with","adjustment")) +
        geom_point(aes_string(x = col1
                              , y = col2
                              , color = "Groups")) +
        geom_segment(aes_string(xend = col1
                                , yend = col2
                                , color = "Groups")
                     , x = 0
                     , y = 0
                     , size = 1
                     , arrow = arrow(length = unit(0.3,"cm"))) +
        geom_label_repel(aes_string(x = col1
                                    , y = col2
                                    , label = "Label")) +
        xlab(paste0("Eigenvector ", col1)) +
        ylab(paste0("Eigenvector ", col2)) +
        theme(plot.title = element_text(hjust = 0.5),
              axis.title = element_text(size = 13),
              legend.text = element_text(size=12)) +
        geom_hline(yintercept = 0, linetype="dashed") +
        geom_vline(xintercept = 0, linetype="dashed")

    })
  })

Note that you did not include the colors that you wanted to use for the groups, so I left the defaults instead.

The plots come out correctly and this should be easier to work through.