Hi Hervé, Thanks for addressing it so quickly, I will check it when the new version if available for biocLite().
Thanks! Jialin On Thu, 2017-09-28 at 13:47 -0700, Hervé Pagès wrote: > Hi Jialin, > > Thanks for the excellent report. These "show" methods like > many others in Bioconductor, rely on low-level helper showAsCell() > which was not working properly on data-frame-like or array-like > objects with a single column, or on SplitDataFrameList objects. > > This should now be addressed. The fix is in S4Vectors 0.14.5 > (release) and 0.15.10 (devel). Both should become available > via biocLite() in about 24 hours. > > Let us know if you still see "show" problems after you update. > > Thanks, > H. > > On 09/28/2017 01:19 AM, Jialin Ma wrote: > > Dear all, > > > > I have a package in reviewing at > > https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Bio > > conductor_Contributions_issues_487&d=DwICAg&c=eRAMFD45gAfqt84VtBcfh > > Q&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=npFXtfKAjVRDigSzn > > tYatjIYfWrBU30MFNqbP6u8Njg&s=P6CWpnkqCx0GPBTlw7QD2gGs_Lc3c063in1J_F > > 4vvDY&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 > > > > _______________________________________________ > > Bioc-devel@r-project.org mailing list > > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_m > > ailman_listinfo_bioc- > > 2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYb > > W0WYiZvSXAJJKaaPhzWA&m=npFXtfKAjVRDigSzntYatjIYfWrBU30MFNqbP6u8Njg& > > s=J5tukPZSuK7728ZillLQJHHrfu7e0o1QsLm0OPNiS2Y&e= > > > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
