Question

ComplexHeatmap - R Session aborted after calling Heatmap()

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AR3513 • 0

@ar3513-11025

Last seen 4.3 years ago

Hi,

I have an error with the following piece of code, which was working fine a few months ago:

Heatmap(score_matrix, cluster_rows = hr, cluster_columns = FALSE,
                         name = "MWAS_score", row_dend_reorder = TRUE)

My R session gets killed, and in the command line it says "Called from: make_cluster(object, "row")". See a description of my variables below:

"score_matrix" is a matrix and looks like:

                        T2D      BMI
Lactate            2.911951 3.963538
3-Hydroxybutyrate  4.177989 0.000000
Leucine            2.402377 3.564122
Valine             2.927309 3.963538
Isoleucine         3.653767 3.228553
Acetate            0.000000 0.000000
Alanine            0.000000 2.910231
1,5-AG            -2.776466 0.000000

and "hr" is of class "hclust" and results from the clustering of the 8 variables in the rows of "score_matrix"*

Any help?

Many thanks,

Andrea

software error Tutorial • 2.5k views

ADD COMMENT • link updated 4.6 years ago by Zuguang Gu ▴ 290 • written 4.6 years ago by AR3513 • 0

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You will likely have to provide more information, like the output of sessionInfo() so we know what versions of the software you are using. But this will still be difficult to get help with as there is we can't reproduce the error to try to help debug

Does this only happen when you provide hr? a. What if you just call Heatmap(score_matrix) b. What if you call it like Heatmap(score_matrix, custer_rows = hr, cluster_columns = FALSE), row_dend_reorder = FALSE)strong text (ie. ignore the `
Does it only happen in RStudio? I can sometimes crash RStudio in fun ways, and I'm not sure it would happen if I just run R from the command line.
Does this still happen after you upgrade to the just-released version of bioconductor?

ADD REPLY • link 4.6 years ago Steve Lianoglou ★ 13k

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Many thanks for your response. See some comments below:

I just realised it works until I use "rowdendreorder = TRUE". So it would work with "Heatmap(scorematrix, clusterrows = hr, cluster_columns = FALSE)"
It crashes both R and RStudio
Yes, I just upgraded bioconductor. See session info below:

sessionInfo() R version 4.0.0 (2020-04-24) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale: [1] enGB.UTF-8/enGB.UTF-8/enGB.UTF-8/C/enGB.UTF-8/en_GB.UTF-8

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

other attached packages: [1] ComplexHeatmap2.4.0 SummarizedExperiment1.18.0 DelayedArray0.14.0
[4] matrixStats0.56.0 Biobase2.48.0 GenomicRanges1.40.0
[7] GenomeInfoDb1.24.0 IRanges2.22.0 S4Vectors0.26.0
[10] BiocGenerics0.34.0 MWASTools_1.5.4

loaded via a namespace (and not attached): [1] KEGGgraph1.48.0 Rcpp1.0.4.6 circlize0.4.8 lattice0.20-41
[5] png0.1-7 Biostrings2.56.0 R62.4.1 cellranger1.1.0
[9] plyr1.8.6 httr1.4.1 ggplot23.3.0 pillar1.4.3
[13] GlobalOptions0.1.1 zlibbioc1.34.0 rlang0.4.5 curl4.3
[17] readxl1.3.1 rstudioapi0.11 data.table1.12.8 car3.0-7
[21] glm21.2.1 GetoptLong0.1.8 Matrix1.2-18 qvalue2.20.0
[25] splines4.0.0 stringr1.4.0 foreign0.8-78 igraph1.2.5
[29] RCurl1.98-1.2 munsell0.5.0 compiler4.0.0 pkgconfig2.0.3
[33] shape1.4.4 KEGGREST1.28.0 gridExtra2.3 tibble3.0.1
[37] GenomeInfoDbData1.2.3 ppcor1.1 rio0.5.16 XML3.99-0.3
[41] crayon1.3.4 MASS7.3-51.5 bitops1.0-6 gtable0.3.0
[45] lifecycle0.2.0 magrittr1.5 scales1.1.0 graph1.66.0
[49] zip2.0.4 stringi1.4.6 carData3.0-3 XVector0.28.0
[53] reshape21.4.4 ellipsis0.3.0 vctrs0.2.4 boot1.3-24
[57] openxlsx4.1.4 RColorBrewer1.1-2 rjson0.2.20 tools4.0.0
[61] forcats0.5.0 glue1.4.0 hms0.5.3 abind1.4-5
[65] clue0.3-57 colorspace1.4-1 cluster2.1.0 haven2.2.0

ADD REPLY • link 4.6 years ago AR3513 • 0

score 1 · Answer 1 · 2020-04-29

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Zuguang Gu ▴ 290

@zuguang-gu-7797

Last seen 27 days ago

Germany / Heidelberg / DKFZ

It is because I forgot to remove one ‘browser()’ line when debug the code. Please update the package to 2.5.1 from github.

ADD COMMENT • link 4.6 years ago Zuguang Gu ▴ 290

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Thanks!! Coul you please update bioconductor level as well? I use the Heatmap function in my package MWASTools, so I get an build error because I can´t run the example that uses your function!

Many thanks

Andrea

ADD REPLY • link 4.6 years ago AR3513 • 0

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It has already updated, both on the release branch and devel branch. It might take several days to appear on bioc website.

ADD REPLY • link 4.6 years ago Zuguang Gu ▴ 290