[Bioc-devel] Printing DataFrame with nested data.frame/DataFrame/DataFrameList

Dear all,

I have a package in reviewing at
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bioconductor_Contributions_issues_487&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=npFXtfKAjVRDigSzntYatjIYfWrBU30MFNqbP6u8Njg&s=P6CWpnkqCx0GPBTlw7QD2gGs_Lc3c063in1J_F4vvDY&e=, in which I
would like to use a GRanges with nested data.frame or DataFrameList to
represent the track data internally.

However, the default show method does not seem to work well with such
structures.

I have an example for GRanges in which one meta-column is a one-column
data frame:

     gr <- GRanges("chr21", IRanges(1:5, width = 1))
     gr$df <- data.frame(x = 1:5)
     show(gr)

     GRanges object with 5 ranges and 1 metadata column:
     Error in .Method(..., deparse.level = deparse.level) :
       number of rows of matrices must match (see arg 3)

However, if the nested data frame has two columns, it can be printed
out correctly:

     gr <- GRanges("chr21", IRanges(1:5, width = 1))
     gr$df <- data.frame(x = 1:5, y = 11:15)
     show(gr)

     GRanges object with 5 ranges and 1 metadata column:
           seqnames    ranges strand |           df
              <Rle> <IRanges>  <Rle> | <data.frame>
       [1]    chr21    [1, 1]      * |         1:11
       [2]    chr21    [2, 2]      * |         2:12
       [3]    chr21    [3, 3]      * |         3:13
       [4]    chr21    [4, 4]      * |         4:14
       [5]    chr21    [5, 5]      * |         5:15
       -------
       seqinfo: 1 sequence from an unspecified genome; no seqlengths

In some cases, it can be printed with a warning message, but the form
is wrong:

     gr <- GRanges("chr21", IRanges(1:5, width = 1), emm = 6:10)
     gr$df <- data.frame(x = 1:5)
     show(gr)

     # The nested df is not printed with correct format, there is only
     # one column in the nested df.

     GRanges object with 5 ranges and 2 metadata columns:
           seqnames    ranges strand |       emm           df
              <Rle> <IRanges>  <Rle> | <integer> <data.frame>
       [1]    chr21    [1, 1]      * |         6    1,2,3,...
       [2]    chr21    [2, 2]      * |         7    1,2,3,...
       [3]    chr21    [3, 3]      * |         8    1,2,3,...
       [4]    chr21    [4, 4]      * |         9    1,2,3,...
       [5]    chr21    [5, 5]      * |        10    1,2,3,...
       -------
       seqinfo: 1 sequence from an unspecified genome; no seqlengths
     Warning message:
     In (function (..., row.names = NULL, check.rows = FALSE, check.names
     = TRUE,  :
       row names were found from a short variable and have been discarded

Nested DataFrameList can not be printed:

     DF <- DataFrame(x = 1:2)
     DF$split = split(DataFrame(aa = 1:4), c(1,1,2,2))
     show(DF)

     DataFrame with 2 rows and 2 columns
     Error in dim(object) <- c(nrow(object), prod(tail(dim(object), -1)))
     :
       invalid first argument

     class(DF$split)

     [1] "CompressedSplitDataFrameList"
     attr(,"package")
     [1] "IRanges"

     In the case above, I understand that it is hard to create a short
     string representation of the nested structure, but I think printing
     dimensions of the nested element may be sufficient.

     Any comments?

     Best,
     Jialin

     -----------
     Session Info:

     R version 3.4.1 (2017-06-30)
     Platform: x86_64-suse-linux-gnu (64-bit)
     Running under: openSUSE Tumbleweed

     Matrix products: default
     BLAS: /usr/lib64/R/lib/libRblas.so
     LAPACK: /usr/lib64/R/lib/libRlapack.so

     locale:
      [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
      [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
      [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
      [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
      [9] LC_ADDRESS=C               LC_TELEPHONE=C
     [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

     attached base packages:
     [1] stats4    parallel  stats     graphics  grDevices
     utils     datasets
     [8] methods   base

     other attached packages:
     [1] Biobase_2.37.2        GenomicRanges_1.29.14 GenomeInfoDb_1.13.4
     [4] IRanges_2.11.17       S4Vectors_0.15.8      BiocGenerics_0.23.1
     [7] magrittr_1.5

     loaded via a namesp

     r$> DF$split <- DF$split %>% as.list %>%
     lapply(as.data.frame)

     r$>
     DF

     DataFrame with 2 rows and 2 columns
               x  split
       <integer> <list>
     1         1    1,2
     2         2    3,4

     ace (and not attached):
     [1]
     zlibbioc_1.23.0         compiler_3.4.1          XVector_0.17.1
     [4] tools_3.4.1             GenomeInfoDbData_0.99.1 RCurl_1.95-
     4.8
     [7] ulimit_0.0-3            bitops_1.0-6