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renozao / NMF

NMF: A Flexible R package for Nonnegative Matrix Factorization
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Combination of breaks and colors does not work #125

Open mhlinder opened 6 years ago

mhlinder commented 6 years ago

Often, I calculate a set of breaks, and a custom color palette.

Just as often, it works to use only the breaks, or only the color palette.

But, when I use both together, aheatmap seems to run out of colors, and recycles them—definitely not working!

Code below and image attached.

aheatmap-colors

mhl:~/$ R

R version 3.5.1 (2018-07-02) -- "Feather Spray"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(NMF)
Loading required package: pkgmaker
Loading required package: registry

Attaching package: ‘pkgmaker’

The following object is masked from ‘package:base’:

    isFALSE

Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [NO: missing Biobase] | Shared memory capabilities [NO: bigmemory] | Cores 7/8
  To enable the Bioconductor layer, try: install.extras('
NMF
') [with Bioconductor repository enabled]
  To enable shared memory capabilities, try: install.extras('
NMF
')
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

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

other attached packages:
[1] NMF_0.21.0      cluster_2.0.7-1 rngtools_1.3.1  pkgmaker_0.27
[5] registry_0.5    colorout_1.2-0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.18       compiler_3.5.1     pillar_1.3.0       RColorBrewer_1.1-2
 [5] plyr_1.8.4         bindr_0.1.1        iterators_1.0.10   tools_3.5.1
 [9] digest_0.6.17      gridBase_0.4-7     tibble_1.4.2       gtable_0.2.0
[13] pkgconfig_2.0.2    rlang_0.2.2        foreach_1.4.4      bibtex_0.4.2
[17] parallel_3.5.1     bindrcpp_0.2.2     withr_2.1.2        stringr_1.3.1
[21] dplyr_0.7.6        grid_3.5.1         tidyselect_0.2.4   glue_1.3.0
[25] R6_2.2.2           reshape2_1.4.3     purrr_0.2.5        ggplot2_3.0.0
[29] magrittr_1.5       scales_1.0.0       codetools_0.2-15   assertthat_0.2.0
[33] xtable_1.8-3       colorspace_1.3-2   stringi_1.2.4      lazyeval_0.2.1
[37] doParallel_1.0.14  munsell_0.5.0      crayon_1.3.4
> set.seed(20181003)
> x <- matrix(rnorm(400), 20)
> range(x)
[1] -3.128249  4.092170
> breaks <- seq(-4, 4, length.out=101)
> cols <- colorRampPalette(c("white", "red"))(100)
> par(mfrow=c(1,3))
> aheatmap(x, Rowv=NA, Colv=NA, color=cols)
> aheatmap(x, Rowv=NA, Colv=NA, breaks=breaks)
> aheatmap(x, Rowv=NA, Colv=NA, breaks=breaks, color=cols)
toddknutson commented 6 years ago

I am also having this problem.

toddknutson commented 6 years ago

I think something happened when the commits from April 16, 2018, or Aug 19, 2018 (bfbe67e2e8c5198ccf77892e381304f8bae96e10 29e165e31eb23c546c47db34e419fab500ad6970 b33a5ba5d1c4bbb00b07b9436a7fe8956dcc51e0 0791ac23c5f7d40af2769d396de4b7ed54e3e200) were applied to the master branch. I restarted a new R session, and installed an older version of NMF before those commits:

library(devtools)
install_github("renozao/NMF#61")

Then your code works correctly:

library(NMF)
set.seed(20181003)
x <- matrix(rnorm(400), 20)
range(x)
breaks <- seq(-4, 4, length.out=101)
cols <- colorRampPalette(c("white", "red"))(100)
pdf("heatmap.pdf", width = 12, height = 4, onefile = FALSE)
par(mfrow=c(1,3))
aheatmap(x, Rowv=NA, Colv=NA, color=cols)
aheatmap(x, Rowv=NA, Colv=NA, breaks=breaks)
aheatmap(x, Rowv=NA, Colv=NA, breaks=breaks, color=cols)
dev.off()

121_hierarchical3

toddknutson commented 5 years ago

However, please note that if you install the GitHub version #61 (see my comment above), the ward clustering method is wrong, as described here: https://github.com/renozao/NMF/issues/117

toddknutson commented 3 years ago

The color breaks problem appears to be solved. I'm not sure when this got resolved. 

# Install the latest version from GitHub
# remotes::install_github("renozao/NMF@d02eba9")
library(NMF)
set.seed(20181003)
x <- matrix(rnorm(400), 20)
range(x)
breaks <- seq(-4, 4, length.out=101)
cols <- colorRampPalette(c("white", "red"))(100)
pdf("heatmap.pdf", width = 12, height = 4, onefile = FALSE)
par(mfrow=c(1,3))
aheatmap(x, Rowv=NA, Colv=NA, color=cols)
aheatmap(x, Rowv=NA, Colv=NA, breaks=breaks)
aheatmap(x, Rowv=NA, Colv=NA, breaks=breaks, color=cols)
dev.off()

heatmap heatmap.pdf

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /panfs/roc/groups/0/lmnp/knut0297/software/modules/openblas/0.3.13/build/lib/libopenblas_zenp-r0.3.13.dev.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] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] RColorBrewer_1.1-2  NMF_0.30.1          Biobase_2.50.0
[4] BiocGenerics_0.36.0 cluster_2.1.0       rngtools_1.5
[7] pkgmaker_0.32.2     registry_0.5-1

loaded via a namespace (and not attached):
 [1] tidyselect_1.1.0  remotes_2.2.0     purrr_0.3.4       reshape2_1.4.4
 [5] colorspace_2.0-0  vctrs_0.3.6       generics_0.1.0    viridisLite_0.3.0
 [9] rlang_0.4.10      pkgbuild_1.2.0    pillar_1.4.7      glue_1.4.2
[13] withr_2.3.0       DBI_1.1.0         foreach_1.5.1     lifecycle_0.2.0
[17] plyr_1.8.6        stringr_1.4.0     munsell_0.5.0     gtable_0.3.0
[21] codetools_0.2-16  callr_3.5.1       doParallel_1.0.16 ps_1.5.0
[25] curl_4.3          fansi_0.4.2       Rcpp_1.0.6        xtable_1.8-4
[29] scales_1.1.1      gridExtra_2.3     ggplot2_3.3.3     digest_0.6.27
[33] stringi_1.5.3     processx_3.4.5    dplyr_1.0.3       rprojroot_2.0.2
[37] grid_4.0.3        cli_2.2.0         tools_4.0.3       magrittr_2.0.1
[41] tibble_3.0.5      crayon_1.3.4      pkgconfig_2.0.3   dendextend_1.14.0
[45] ellipsis_0.3.1    gridBase_0.4-7    prettyunits_1.1.1 assertthat_0.2.1
[49] viridis_0.5.1     iterators_1.0.13  R6_2.5.0          compiler_4.0.3