Questions about heatmap table function #22
Comments
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It's not normal! Could you share your input data? I can double-check this from my side. Thanks! p.s. Sorry for the delayed response. The notification keeps getting lost somehow. ;( |
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Hi, many thanks for your reply! I just run the codes listed on the website. |
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Hi @HelloWorldLTY, |
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@HelloWorldLTY you mentioned you were using a GPU, is that correct or is it a typo for CPU? |
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Also, could you try running the following benchmark? It would help to be sure that your time is actually being spent evaluating the heatmapTable function, and not something else cluster scheduling-related. It should produce the output below, although if it really takes an hour to make each heatmap this won't finish in any reasonable amount of time. But in my benchmarking it only takes ~20ms per function call. BiocManager::version()
#> [1] '3.15'
BiocManager::valid()
#> 'getOption("repos")' replaces Bioconductor standard repositories, see
#> '?repositories' for details
#>
#> replacement repositories:
#> CRAN: https://cloud.r-project.org
#> Warning: 0 packages out-of-date; 39 packages too new
#>
#> * sessionInfo()
#>
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#>
#> 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] stats graphics grDevices utils datasets methods base
#>
#> loaded via a namespace (and not attached):
#> [1] rstudioapi_0.13 knitr_1.39 magrittr_2.0.3
#> [4] R.cache_0.15.0 rlang_1.0.4 fastmap_1.1.0
#> [7] fansi_1.0.3 stringr_1.4.0 styler_1.7.0
#> [10] highr_0.9 tools_4.2.1 xfun_0.31
#> [13] R.oo_1.25.0 utf8_1.2.2 cli_3.3.0
#> [16] withr_2.5.0 htmltools_0.5.2 ellipsis_0.3.2
#> [19] yaml_2.3.5 digest_0.6.29 tibble_3.1.7
#> [22] lifecycle_1.0.1 crayon_1.5.1 BiocManager_1.30.18
#> [25] purrr_0.3.4 R.utils_2.12.0 vctrs_0.4.1
#> [28] fs_1.5.2 glue_1.6.2 evaluate_0.15
#> [31] rmarkdown_2.14 reprex_2.0.1 stringi_1.7.8
#> [34] compiler_4.2.1 pillar_1.7.0 R.methodsS3_1.8.2
#> [37] pkgconfig_2.0.3
#>
#> Bioconductor version '3.15'
#>
#> * 0 packages out-of-date
#> * 39 packages too new
#>
#> create a valid installation with
#>
#> BiocManager::install(c(
#> "annotation", "AnnotationDbi", "AnnotationHub", "beachmat", "Biobase",
#> "BiocFileCache", "BiocGenerics", "BiocNeighbors", "BiocParallel",
#> "BiocSingular", "BioPlex", "Biostrings", "curatedMetagenomicData",
#> "DECIPHER", "decontam", "DelayedArray", "DelayedMatrixStats",
#> "DirichletMultinomial", "ExperimentHub", "GenomeInfoDb", "GenomicRanges",
#> "HGNChelper", "interactiveDisplayBase", "IRanges", "KEGGREST",
#> "MatrixGenerics", "mia", "MultiAssayExperiment", "S4Vectors",
#> "ScaledMatrix", "scater", "scuttle", "SingleCellExperiment",
#> "sparseMatrixStats", "SummarizedExperiment", "treeio",
#> "TreeSummarizedExperiment", "XVector", "zlibbioc"
#> ), update = TRUE, ask = FALSE)
#>
#> more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date
suppressPackageStartupMessages({
library(GenomicSuperSignature)
library(bcellViper)
library(microbenchmark)
})
RAVmodel <- getModel("PLIERpriors", load = TRUE)
#> [1] "downloading"
data(bcellViper)
dset
#> ExpressionSet (storageMode: lockedEnvironment)
#> assayData: 6249 features, 211 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: GSM44075 GSM44078 ... GSM44302 (211 total)
#> varLabels: sampleID description detailed_description
#> varMetadata: labelDescription
#> featureData: none
#> experimentData: use 'experimentData(object)'
#> Annotation:
val_all <- validate(dset, RAVmodel)
suppressMessages({
microbenchmark(heatmapTable(
val_all,
RAVmodel,
num.out = 5,
swCutoff = 0
))
})
#> Unit: milliseconds
#> expr min lq
#> heatmapTable(val_all, RAVmodel, num.out = 5, swCutoff = 0) 18.1544 18.87651
#> mean median uq max neval
#> 21.89993 19.24291 21.69203 113.4549 100
sessionInfo()
#> R version 4.2.1 (2022-06-23)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 20.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
#>
#> 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 stats graphics grDevices utils datasets methods
#> [8] base
#>
#> other attached packages:
#> [1] microbenchmark_1.4.9 bcellViper_1.32.0
#> [3] GenomicSuperSignature_1.4.0 SummarizedExperiment_1.27.1
#> [5] Biobase_2.57.1 GenomicRanges_1.49.0
#> [7] GenomeInfoDb_1.33.3 IRanges_2.31.0
#> [9] S4Vectors_0.35.1 BiocGenerics_0.43.0
#> [11] MatrixGenerics_1.9.0 matrixStats_0.62.0
#>
#> loaded via a namespace (and not attached):
#> [1] TH.data_1.1-1 colorspace_2.0-3 ggsignif_0.6.3
#> [4] rjson_0.2.21 ellipsis_0.3.2 circlize_0.4.15
#> [7] XVector_0.37.0 GlobalOptions_0.1.2 fs_1.5.2
#> [10] clue_0.3-61 rstudioapi_0.13 ggpubr_0.4.0
#> [13] bit64_4.0.5 mvtnorm_1.1-3 fansi_1.0.3
#> [16] splines_4.2.1 codetools_0.2-18 R.methodsS3_1.8.2
#> [19] doParallel_1.0.17 cachem_1.0.6 knitr_1.39
#> [22] broom_1.0.0 cluster_2.1.3 dbplyr_2.2.1
#> [25] png_0.1-7 R.oo_1.25.0 BiocManager_1.30.18
#> [28] readr_2.1.2 compiler_4.2.1 httr_1.4.3
#> [31] backports_1.4.1 assertthat_0.2.1 Matrix_1.4-1
#> [34] fastmap_1.1.0 cli_3.3.0 htmltools_0.5.2
#> [37] tools_4.2.1 gtable_0.3.0 glue_1.6.2
#> [40] GenomeInfoDbData_1.2.8 dplyr_1.0.9 rappdirs_0.3.3
#> [43] Rcpp_1.0.9 carData_3.0-5 styler_1.7.0
#> [46] vctrs_0.4.1 iterators_1.0.14 xfun_0.31
#> [49] stringr_1.4.0 lifecycle_1.0.1 rstatix_0.7.0
#> [52] MASS_7.3-58 zoo_1.8-10 zlibbioc_1.43.0
#> [55] scales_1.2.0 hms_1.1.1 parallel_4.2.1
#> [58] sandwich_3.0-2 RColorBrewer_1.1-3 ComplexHeatmap_2.12.0
#> [61] yaml_2.3.5 curl_4.3.2 memoise_2.0.1
#> [64] ggplot2_3.3.6 stringi_1.7.8 RSQLite_2.2.14
#> [67] highr_0.9 foreach_1.5.2 filelock_1.0.2
#> [70] shape_1.4.6 rlang_1.0.4 pkgconfig_2.0.3
#> [73] bitops_1.0-7 evaluate_0.15 lattice_0.20-45
#> [76] purrr_0.3.4 bit_4.0.4 tidyselect_1.1.2
#> [79] magrittr_2.0.3 R6_2.5.1 magick_2.7.3
#> [82] generics_0.1.3 multcomp_1.4-19 DelayedArray_0.23.0
#> [85] DBI_1.1.3 pillar_1.7.0 withr_2.5.0
#> [88] survival_3.3-1 abind_1.4-5 RCurl_1.98-1.7
#> [91] tibble_3.1.7 crayon_1.5.1 car_3.1-0
#> [94] utf8_1.2.2 BiocFileCache_2.5.0 tzdb_0.3.0
#> [97] rmarkdown_2.14 GetoptLong_1.0.5 grid_4.2.1
#> [100] blob_1.2.3 reprex_2.0.1 digest_0.6.29
#> [103] R.cache_0.15.0 tidyr_1.2.0 R.utils_2.12.0
#> [106] munsell_0.5.0Created on 2022-07-15 by the reprex package (v2.0.1) |
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Hi, thanks for your help. replacement repositories: Bioconductor version 3.14 (BiocManager 1.30.18), R 4.1.3 (2022-03-10) Warning message: Updating HTML index of packages in '.Library' Making 'packages.html' ... Old packages: 'bslib', 'callr', 'farver', 'gert', 'lme4', 'MASS', 'processx', Updating HTML index of packages in '.Library' Making 'packages.html' ... ✖ Install the styler package in order to use ℹ Non-interactive session, setting ℹ Rendering reprex... CLIPR_ALLOW has not been set, so clipr will not run interactively` Could you please help me solve it? Thanks a lot. |
Hi, I found that this step took me a pretty long time to run:
I waited for more than one hour with one 30 GB GPU from an HPC. Is it normal? Thanks a lot.
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