[BUG] Rounding removes DETable sorting

[csoneson]

Changing the number of significant digits in a DETable undoes any sorting that has been done before.

Example:

library(iSEEde)
library(airway)
library(DESeq2)
library(iSEE)

data("airway")
airway$dex <- relevel(airway$dex, "untrt")
dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
dds <- DESeq(dds)
res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
iSEE(airway, initial = list(
    DETable(ContrastName="dex: trt vs untrt")
))

• Sort by baseMean
• Check 'Round digits'

-> table is unsorted

R session information

Session info

─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.1 (2023-06-16)
 os       macOS Ventura 13.5.1
 system   aarch64, darwin20
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Europe/Zurich
 date     2023-09-06
 rstudio  2023.06.1+524 Mountain Hydrangea (desktop)
 pandoc   3.1.7 @ /opt/homebrew/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-5     2016-07-21 [1] CRAN (R 4.3.0)
 airway               * 1.21.0    2023-04-27 [1] Bioconductor
 Biobase              * 2.61.0    2023-06-02 [1] Bioconductor
 BiocGenerics         * 0.47.0    2023-06-02 [1] Bioconductor
 BiocParallel           1.35.4    2023-08-17 [1] Bioconductor
 bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.3.0)
 bslib                  0.5.1     2023-08-11 [1] CRAN (R 4.3.0)
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 cli                    3.6.1     2023-03-23 [1] CRAN (R 4.3.0)
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 crayon                 1.5.2     2022-09-29 [1] CRAN (R 4.3.0)
 DelayedArray           0.27.10   2023-07-28 [1] Bioconductor
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 digest                 0.6.33    2023-07-07 [1] CRAN (R 4.3.0)
 doParallel             1.0.17    2022-02-07 [1] CRAN (R 4.3.0)
 dplyr                  1.1.3     2023-09-03 [1] CRAN (R 4.3.0)
 DT                     0.29      2023-08-29 [1] CRAN (R 4.3.0)
 edgeR                  3.43.8    2023-08-02 [1] Bioconductor
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 generics               0.1.3     2022-07-05 [1] CRAN (R 4.3.0)
 GenomeInfoDb         * 1.37.3    2023-08-28 [1] Bioconductor
 GenomeInfoDbData       1.2.10    2023-05-03 [1] Bioconductor
 GenomicRanges        * 1.53.1    2023-06-02 [1] Bioconductor
 GetoptLong             1.0.5     2020-12-15 [1] CRAN (R 4.3.0)
 ggplot2                3.4.3     2023-08-14 [1] CRAN (R 4.3.0)
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 GlobalOptions          0.1.2     2020-06-10 [1] CRAN (R 4.3.0)
 glue                   1.6.2     2022-02-24 [1] CRAN (R 4.3.0)
 gtable                 0.3.4     2023-08-21 [1] CRAN (R 4.3.0)
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 httpuv                 1.6.11    2023-05-11 [1] CRAN (R 4.3.0)
 igraph                 1.5.1     2023-08-10 [1] CRAN (R 4.3.0)
 IRanges              * 2.35.2    2023-06-23 [1] Bioconductor
 iSEE                 * 2.13.5    2023-07-26 [1] Bioconductor
 iSEEde               * 0.99.0    2023-05-18 [1] Github (iSEE/iSEEde@dc2eb18)
 iterators              1.0.14    2022-02-05 [1] CRAN (R 4.3.0)
 jquerylib              0.1.4     2021-04-26 [1] CRAN (R 4.3.0)
 jsonlite               1.8.7     2023-06-29 [1] CRAN (R 4.3.0)
 later                  1.3.1     2023-05-02 [1] CRAN (R 4.3.0)
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 limma                  3.57.7    2023-08-02 [1] Bioconductor
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 rstudioapi             0.15.0    2023-07-07 [1] CRAN (R 4.3.0)
 S4Arrays               1.1.6     2023-08-31 [1] Bioconductor
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 SparseArray            1.1.12    2023-08-31 [1] Bioconductor
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 [1] /Users/charlottesoneson/Documents/Software/Rlib/Bioc3.18
 [2] /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library

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[kevinrue]

Oh.

That might be out of our hands, as the sorting is happening inside the JS table itself, not controlled/tracked by iSEE.

That said, wouldn't be the first we wiggle our way into the JS code to take control of some things ourselves. (Consulting for Posit, anyone? ^^)