ComplexHeatmap column dendrogram
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Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States

The current version of ComplexHeatmap sometimes fails to correctly draw the column dendrogram. As an example, using these data, I get the following heatmap:

And if I use an older version, I get this:

For the current (non working version):

> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /data/oldR/R-3.4.2/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-3.4.2/lib64/R/lib/libRlapack.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] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] ComplexHeatmap_1.17.1

loaded via a namespace (and not attached):
[1] colorspace_1.3-2     compiler_3.4.2       rjson_0.2.15        
[4] circlize_0.4.3       tools_3.4.2          GlobalOptions_0.0.12
[7] RColorBrewer_1.1-2   GetoptLong_0.1.6     shape_1.4.4  

 

And for the version that does work:

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /data/oldR/R-3.4.0/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-3.4.0/lib64/R/lib/libRlapack.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] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] ComplexHeatmap_1.14.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12         compiler_3.4.0       DEoptimR_1.0-8      
 [4] RColorBrewer_1.1-2   plyr_1.8.4           viridis_0.4.0       
 [7] class_7.3-14         tools_3.4.0          prabclus_2.2-6      
[10] dendextend_1.5.2     mclust_5.3           viridisLite_0.2.0   
[13] tibble_1.3.4         gtable_0.2.0         lattice_0.20-35     
[16] rlang_0.1.2          mvtnorm_1.0-6        gridExtra_2.3       
[19] trimcluster_0.1-2    cluster_2.0.6        GlobalOptions_0.0.12
[22] fpc_2.1-10           stats4_3.4.0         diptest_0.75-7      
[25] nnet_7.3-12          robustbase_0.92-7    GetoptLong_0.1.6    
[28] flexmix_2.3-14       ggplot2_2.2.1        kernlab_0.9-25      
[31] magrittr_1.5         whisker_0.3-2        scales_0.5.0        
[34] modeltools_0.2-21    MASS_7.3-47          shape_1.4.3         
[37] circlize_0.4.1       colorspace_1.3-2     lazyeval_0.2.0      
[40] munsell_0.4.3        rjson_0.2.15        
>
complexheatmap • 794 views
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Entering edit mode
jokergoo ▴ 130
@jokergoo-8506
Last seen 9 weeks ago
Germany

That was a bug that I can remember how it came to some versions of the package. I have fixed it recently. Please the newest version from GitHub (devtools::install_github("jokergoo/ComplexHeatmap").

 

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Entering edit mode

If it's a bug then you should push the fix to the release version as well.

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