const-ae/ggupset

Error in `[.default`(x, i) : invalid subscript type 'list'

taylorreiter opened this issue · 3 comments

taylorreiter commented

I have successfully run the test data:

library(dplyr)
library(ggplot2)
library(purrr)
library(readr)
library(wesanderson)
library(ggupset)

tidy_movies %>%
  distinct(title, year, length, .keep_all=TRUE) %>%
  ggplot(aes(x=Genres)) +
  geom_bar() +
  scale_x_upset(n_intersections = 20)

but when I try and use similar code on my own data, and get the error:

Error in `[.default`(x, i) : invalid subscript type 'list'

The code I'm running on my dataset looks like this:

all %>%
  distinct(name, .keep_all=TRUE) %>%
  ggplot(aes(x=source)) +
  geom_bar() +
  scale_x_upset()

And head() of my data looks like this:

# A tibble: 6 x 2
  source name                                                                                                
  <chr>  <chr>                                                                                               
1 iHMP   JH590866.1 Lachnospiraceae bacterium 7_1_58FAA genomic scaffold supercont1.1, whole genome shotgun …
2 iHMP   HGM_v1.0_all_60664_fna/SRS1719498_9.fna                                                             
3 iHMP   HGM_v1.0_all_60664_fna/SRS294916_20.fna                                                             
4 iHMP   HGM_v1.0_all_60664_fna/ERS396297_11.fna                                                             
5 iHMP   HGM_v1.0_all_60664_fna/SRS1719577_6.fna                                                             
6 SRP1   HGM_v1.0_all_60664_fna/SRS1719577_6.fna

Is there an obvious reason for this error that I am missing?

My sessionInfo() is:

R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.2

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggupset_0.1.0      readr_1.3.1        purrr_0.3.3        ggplot2_3.3.0.9000 dplyr_0.8.5       
[6] testthat_2.3.2     devtools_2.2.2     usethis_1.5.1     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3        compiler_3.6.2    pillar_1.4.3      prettyunits_1.1.1 remotes_2.1.1    
 [6] tools_3.6.2       digest_0.6.25     pkgbuild_1.0.6    pkgload_1.0.2     memoise_1.1.0    
[11] tibble_2.1.3      lifecycle_0.2.0   gtable_0.3.0      pkgconfig_2.0.3   rlang_0.4.5      
[16] cli_2.0.2         rstudioapi_0.11   withr_2.1.2       vctrs_0.2.3       hms_0.5.3        
[21] desc_1.2.0        fs_1.3.2          rprojroot_1.3-2   grid_3.6.2        tidyselect_1.0.0 
[26] glue_1.3.1        R6_2.4.1          processx_3.4.2    fansi_0.4.1       sessioninfo_1.1.1
[31] callr_3.4.2       magrittr_1.5      backports_1.1.5   scales_1.1.0      ps_1.3.2         
[36] ellipsis_0.3.0    assertthat_0.2.1  colorspace_1.4-1  munsell_0.5.0     crayon_1.3.4
const-ae commented

Hi Taylor,

thanks for the extensive bug report. I can reproduce the problem with the following code:

library(tidyverse)
library(ggupset)  
all <- tibble(source = c(rep("iHMP", 5), "SRP1"),
              name = LETTERS[1:6])
all
#> # A tibble: 6 x 2
#>   source name 
#>   <chr>  <chr>
#> 1 iHMP   A    
#> 2 iHMP   B    
#> 3 iHMP   C    
#> 4 iHMP   D    
#> 5 iHMP   E    
#> 6 SRP1   F
all %>%
  distinct(name, .keep_all=TRUE) %>%
  ggplot(aes(x=source)) +
  geom_bar() +
  scale_x_upset()
#> Error in `[.default`(x, i): invalid subscript type 'list'

Created on 2020-03-27 by the reprex package (v0.3.0)

I don't know where it's coming from, but I will investigate what could be the root cause. It might be related to the recent update of ggplot2 to version 3.3.0.

const-ae commented

Okay, it actually turned out to be a minor problem. You pass a character vector to aes(x = source). ggupset, however, expects a list. The solution to fix your problem is

library(tidyverse)
library(ggupset)
  all <- tibble(source = c(rep("iHMP", 5), "SRP1"),
                name = LETTERS[1:6])
  # Informative Error message
  all %>%
    distinct(name, .keep_all=TRUE) %>%
    ggplot(aes(x=source)) +
    geom_bar() +
    scale_x_upset()
#> Error in f(..., self = self): Error in scale_upset for aesthetic 'x'. 'x' must be of type list. It currently is: character
  
  # Works:
  all %>%
    distinct(name, .keep_all=TRUE) %>%
    mutate(source = as.list(source)) %>%
    ggplot(aes(x=source)) +
    geom_bar() +
    scale_x_upset()
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?
#> geom_path: Each group consists of only one observation. Do you need to adjust
#> the group aesthetic?

Created on 2020-03-29 by the reprex package (v0.3.0)

However, the original error message was really confusing. I have fixed the issue and ggupset now returns a more helpful explanation what goes wrong if you call scale_x_upset() with a character vector.

taylorreiter commented

Ah this makes sense...thank you so much, I love the more informative error message!

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