Error in if (all(abs(as.numeric(labels_y) - as.numeric(y)) < 1e-04)) { : missing value where TRUE/FALSE needed

[denvercal1234GitHub]

Hi there,

When running CATALYST::plotExprHeatmap I encountered the error below for some proteins.

Would you mind giving me some pointers to solve this error?

When I took out q=0 then there was no error.

Thank you for your help.

CATALYST::plotExprHeatmap(F37_sce, features = "CD185", scale = "first", q = 0, bars = T, k="meta29", by="cluster_id", perc=T, bin_anno = T)

Error in if (all(abs(as.numeric(labels_y) - as.numeric(y)) < 1e-04)) { : 
  missing value where TRUE/FALSE needed

> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.3.0 (2023-04-21)
 os       Ubuntu 22.04.2 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_GB.UTF-8
 ctype    en_GB.UTF-8
 tz       Europe/London
 date     2023-06-29
 rstudio  2023.03.1+446 Cherry Blossom (server)
 pandoc   2.19.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 abind                  1.4-5      2016-07-21 [2] CRAN (R 4.3.0)
 askpass                1.1        2019-01-13 [2] CRAN (R 4.3.0)
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 beachmat               2.16.0     2023-04-25 [2] Bioconductor
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 Biobase              * 2.60.0     2023-04-25 [2] Bioconductor
 BiocGenerics         * 0.46.0     2023-04-25 [2] Bioconductor
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 BiocNeighbors          1.18.0     2023-04-25 [2] Bioconductor
 BiocParallel         * 1.34.2     2023-05-22 [2] Bioconductor
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 Cairo                  1.6-0      2022-07-05 [2] CRAN (R 4.3.0)
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 caret                * 6.0-94     2023-03-21 [2] CRAN (R 4.3.0)
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 ComplexHeatmap       * 2.16.0     2023-04-25 [2] Bioconductor
 ConsensusClusterPlus   1.64.0     2023-04-25 [2] Bioconductor
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 CytoNorm             * 0.0.17     2023-06-29 [1] Github (saeyslab/CytoNorm@5aa8942)
 data.table           * 1.14.8     2023-02-17 [2] CRAN (R 4.3.0)
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 flowViz              * 1.64.0     2023-04-25 [2] Bioconductor
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 [1] /ceph/home/q/qnguyen/R/x86_64-pc-linux-gnu-library/4.3
 [2] /ceph/package/u22/R-cbrg/current/4.3.0
 [3] /ceph/package/u22/R-base/4.3.0/lib/R/library

[HelenaLC]

Hm. I can't reproduce this from the information you provided. Here some thoughts...

• Setting q = 0 will basically amount to 1. scaling values between 0 and 1 using expression minima and maxima, respectively; and, 2. taking the median per cluster for visualization.
• The check resulting in the error (if (all(abs(as.numeric(labels_y) - as.numeric(y)) < 1e-04))) is not in CATALYSTs code base, and I'm assuming it's ComplexHeatmap that does it (you could check via running traceback() what function call exactly is causing the error).
• If so, I am not sure which labels are being referred to here, but that would be worth tracking down, e.g., does q = 0.01, bin_anno = FALSE give an error? Because I'd assuming only bin values are affected by q (not, say, the cluster frequency bars). Then, it might be something's off with the scaling, e.g., perhaps some proteins are 0-ish everywhere?

[HelenaLC]

closing due to inactivity; please comment back if the issue persists/is still of interest.