Question: Error when using multiple heatmaps in ComplexHeatmaps
0
gravatar for brt381
2.7 years ago by
brt3810
Canada
brt3810 wrote:

 

I am having difficulty with creating multiple heatmaps with the ComplexHeatmap package. When I run a script that contains code exactly lifted from the documentation (https://bioconductor.org/packages/release/bioc/vignettes/ComplexHeatmap/inst/doc/s3.a_list_of_heatmaps.html)...

library(ComplexHeatmap)

mat1 = matrix(rnorm(80, 2), 8, 10)
mat1 = rbind(mat1, matrix(rnorm(40, -2), 4, 10))
rownames(mat1) = paste0("R", 1:12)
colnames(mat1) = paste0("C", 1:10)

mat2 = matrix(rnorm(60, 2), 6, 10)
mat2 = rbind(mat2, matrix(rnorm(60, -2), 6, 10))
rownames(mat2) = paste0("R", 1:12)
colnames(mat2) = paste0("C", 1:10)

ht1 = Heatmap(mat1, name = "ht1")
ht2 = Heatmap(mat2, name = "ht2")
class(ht1)

class(ht2)
sessionInfo()
ht1 + ht2

... I get the error message:

Error in ht1 + ht2 : non-numeric argument to binary operator
Execution halted

Here is the output of sessionInfo():

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.2

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
[1] ComplexHeatmap_1.12.0

loaded via a namespace (and not attached):
 [1] flexmix_2.3-13       Rcpp_0.12.9          cluster_2.0.5       
 [4] whisker_0.3-2        magrittr_1.5         fpc_2.1-10          
 [7] MASS_7.3-45          munsell_0.4.3        mclust_5.2.1        
[10] colorspace_1.3-2     lattice_0.20-34      rjson_0.2.15        
[13] plyr_1.8.4           prabclus_2.2-6       tools_3.3.2         
[16] nnet_7.3-12          gtable_0.2.0         circlize_0.3.9      
[19] class_7.3-14         modeltools_0.2-21    lazyeval_0.2.0      
[22] assertthat_0.1       tibble_1.2           kernlab_0.9-25      
[25] trimcluster_0.1-2    RColorBrewer_1.1-2   ggplot2_2.2.1       
[28] GlobalOptions_0.0.10 dendextend_1.3.0     robustbase_0.92-7   
[31] shape_1.4.2          DEoptimR_1.0-8       methods_3.3.2       
[34] scales_0.4.1         diptest_0.75-7       stats4_3.3.2        
[37] mvtnorm_1.0-5        GetoptLong_0.1.5    
bug complexheatmap • 596 views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by brt3810
Answer: Error when using multiple heatmaps in ComplexHeatmaps
1
gravatar for brt381
2.7 years ago by
brt3810
Canada
brt3810 wrote:

OK, this seems very strange. I was previously running the code I posted using Rscript, and it gives the indicated error. But when I run R interactively and copy-and-paste those lines in, it does work (with or without --vanilla). It does NOT work via Rscript whether with or without --vanilla.

EDIT: I did some Googling and it was suggested to say library(methods) at the top of the script (apparently R attaches this by default, but not Rscript). This made it work in Rscript!

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by brt3810
Answer: Error when using multiple heatmaps in ComplexHeatmaps
0
gravatar for James W. MacDonald
2.7 years ago by
United States
James W. MacDonald51k wrote:

I can't reproduce. You might try restarting R and re-running your code, particularly with R --vanilla to get a clean workspace on startup. If you still get an error, please show the results from

traceback()
ADD COMMENTlink written 2.7 years ago by James W. MacDonald51k
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