[feature request] add .drop argument to group_by, e.g. to include empty seqlevels

[jayoung]

Hi there,

I only just discovered your package - I'm excited to start being tidy with my GRanges!

Apologies if I missed something, but I think I am requesting an enhancement.

With tibbles, when I'm grouping on a factor, there's a way to summarize and make sure I include empty groups, by using the .drop=FALSE argument. But for GRanges, I don't see a way to include the empty groups. Again, sorry if I missed it - I have tried searching but didn't see anything.

I've provided code below that I think is a nice small example.

thanks very much,

Janet Young

Malik lab,
Fred Hutch Cancer Research Center,
Seattle, WA

## here's how I include empty groups when summarizing a tibble
library(tidyverse)
fruit_tbl <- data.frame(fruit=factor( c("apple","apple","orange","pear"), 
                                      levels=c("apple","orange","pear","banana")),
                        weight=c(3,4,5,3)) %>% 
    as_tibble()
# we DO get output for 'banana', the empty group:
fruit_tbl %>% 
    group_by(fruit, .drop=FALSE) %>% 
    summarise(numFruits=n(), 
              mean=mean(weight))
#   A tibble: 4 × 3
#   fruit  numFruits  mean
#   <fct>      <int> <dbl>
# 1 apple          2   3.5
# 2 orange         1   5  
# 3 pear           1   3  
# 4 banana         0 NaN  

But I don't see a way to include empty groups in plyranges. Is that true? Sorry if I missed it. I am using plyranges_1.14.0 (release version). Here's what I tried (after restarting R to make sure tidyverse packages aren't loaded):

library(plyranges)

## make GRanges where not all factor levels are represented (for seqnames, also for regionType)
grng2 <- data.frame(seqnames = sample(c("chr1", "chr2"), 7, replace = TRUE),
                   strand = sample(c("+", "-"), 7, replace = TRUE),
                   gc = runif(7),
                   start = 1:7,
                   width = 10) %>%
    mutate(seqnames=factor(seqnames, levels=c("chr1", "chr2", "chr3"))) %>% 
    mutate(regionType=factor( sample(c("a", "b"), 7, replace = TRUE),
                              levels=c("a", "b", "c"))) %>% 
    as_granges()

## works, but we don't get summaries for the empty levels of seqlevel (chr3) or regionType (c):
grng2 %>% 
    group_by(seqnames) %>% 
    summarize(numRegions=n(),
              meanGC=mean(gc))
# DataFrame with 2 rows and 3 columns
#   seqnames numRegions    meanGC
#      <Rle>  <integer> <numeric>
# 1     chr1          6  0.592756
# 2     chr2          1  0.664616


grng2 %>% 
    group_by(regionType) %>% 
    summarize(numRegions=n(),
              meanGC=mean(gc))
# DataFrame with 2 rows and 3 columns
#   regionType numRegions    meanGC
#    <factor>  <integer> <numeric>
# 1          a          6  0.646677
# 2          b          1  0.341085

## can't use .drop like I would with a tibble
grng2 %>% 
    group_by(regionType, .drop=FALSE) %>% 
    summarize(numRegions=n(),
              meanGC=mean(gc))
# Error in new_grouping(.data, ...) : Column `.drop` is unknown

and here's my R session information

library(sessioninfo)
sessioninfo::session_info()
─ Session info ─────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       macOS Monterey 12.2.1
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Los_Angeles
 date     2022-02-23
 rstudio  1.4.1717 Juliet Rose (desktop)
 pandoc   NA

─ Packages ─────────────────────────────────────────────────────────────────────────────────
 package              * version  date (UTC) lib source
 assertthat             0.2.1    2019-03-21 [1] CRAN (R 4.1.0)
 Biobase                2.54.0   2021-10-26 [1] Bioconductor
 BiocGenerics         * 0.40.0   2021-10-26 [1] Bioconductor
 BiocIO                 1.4.0    2021-10-26 [1] Bioconductor
 BiocParallel           1.28.3   2021-12-09 [1] Bioconductor
 Biostrings             2.62.0   2021-10-26 [1] Bioconductor
 bitops                 1.0-7    2021-04-24 [1] CRAN (R 4.1.0)
 cli                    3.1.1    2022-01-20 [1] CRAN (R 4.1.2)
 crayon                 1.4.2    2021-10-29 [1] CRAN (R 4.1.0)
 DBI                    1.1.2    2021-12-20 [1] CRAN (R 4.1.1)
 DelayedArray           0.20.0   2021-10-26 [1] Bioconductor
 dplyr                  1.0.7    2021-06-18 [1] CRAN (R 4.1.0)
 ellipsis               0.3.2    2021-04-29 [1] CRAN (R 4.1.0)
 fansi                  1.0.2    2022-01-14 [1] CRAN (R 4.1.2)
 generics               0.1.2    2022-01-31 [1] CRAN (R 4.1.2)
 GenomeInfoDb         * 1.30.0   2021-10-26 [1] Bioconductor
 GenomeInfoDbData       1.2.7    2021-11-16 [1] Bioconductor
 GenomicAlignments      1.30.0   2021-10-26 [1] Bioconductor
 GenomicRanges        * 1.46.1   2021-11-18 [1] Bioconductor
 glue                   1.6.1    2022-01-22 [1] CRAN (R 4.1.2)
 IRanges              * 2.28.0   2021-10-26 [1] Bioconductor
 lattice                0.20-45  2021-09-22 [1] CRAN (R 4.1.2)
 lifecycle              1.0.1    2021-09-24 [1] CRAN (R 4.1.0)
 magrittr               2.0.2    2022-01-26 [1] CRAN (R 4.1.2)
 Matrix                 1.4-0    2021-12-08 [1] CRAN (R 4.1.0)
 MatrixGenerics         1.6.0    2021-10-26 [1] Bioconductor
 matrixStats            0.61.0   2021-09-17 [1] CRAN (R 4.1.0)
 pillar                 1.7.0    2022-02-01 [1] CRAN (R 4.1.2)
 pkgconfig              2.0.3    2019-09-22 [1] CRAN (R 4.1.0)
 plyranges            * 1.14.0   2021-10-26 [1] Bioconductor
 purrr                  0.3.4    2020-04-17 [1] CRAN (R 4.1.0)
 R6                     2.5.1    2021-08-19 [1] CRAN (R 4.1.0)
 RCurl                  1.98-1.5 2021-09-17 [1] CRAN (R 4.1.0)
 restfulr               0.0.13   2017-08-06 [1] CRAN (R 4.1.0)
 rjson                  0.2.21   2022-01-09 [1] CRAN (R 4.1.2)
 rlang                  1.0.1    2022-02-03 [1] CRAN (R 4.1.2)
 Rsamtools              2.10.0   2021-10-26 [1] Bioconductor
 rstudioapi             0.13     2020-11-12 [1] CRAN (R 4.1.0)
 rtracklayer            1.54.0   2021-10-26 [1] Bioconductor
 S4Vectors            * 0.32.3   2021-11-21 [1] Bioconductor
 sessioninfo          * 1.2.2    2021-12-06 [1] CRAN (R 4.1.0)
 SummarizedExperiment   1.24.0   2021-10-26 [1] Bioconductor
 tibble                 3.1.6    2021-11-07 [1] CRAN (R 4.1.0)
 tidyselect             1.1.1    2021-04-30 [1] CRAN (R 4.1.0)
 utf8                   1.2.2    2021-07-24 [1] CRAN (R 4.1.0)
 vctrs                  0.3.8    2021-04-29 [1] CRAN (R 4.1.0)
 XML                    3.99-0.8 2021-09-17 [1] CRAN (R 4.1.0)
 XVector                0.34.0   2021-10-26 [1] Bioconductor
 yaml                   2.2.2    2022-01-25 [1] CRAN (R 4.1.2)
 zlibbioc               1.40.0   2021-10-26 [1] Bioconductor

 [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library