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talgalili / heatmaply

Interactive Heat Maps for R Using plotly
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Error with two column dataframe #32

Closed bextra closed 7 years ago

bextra commented 7 years ago

(I think I filed this on the dextend package first on accident, so posting correctly here)

I am trying to plot a simple two columned dataframe and receive the following error:

Error: all(vapply(s, is.integer, NA)) is not TRUE

The dataframe I'm working with has two columns each with class = integer so I'm not seeing where this would come from. I have attached a subset of the df that still creates the issue.

load("example_df.Rda")
heatmaply(example_df)

Any help would be greatly appreciated. Below is version and session info.

example_df.Rda.zip

R version:

platform       x86_64-redhat-linux-gnu
arch           x86_64
os             linux-gnu
system         x86_64, linux-gnu
status
major          3
minor          2.3
year           2015
month          12
day            10
svn rev        69752
language       R
version.string R version 3.2.3 (2015-12-10)
nickname       Wooden Christmas-Tree

SessionInfo

R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

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] stringi_1.1.2   heatmaply_0.6.0 viridis_0.3.4   plotly_4.5.6
[5] ggplot2_2.2.1

loaded via a namespace (and not attached):
 [1] gtools_3.5.0       modeltools_0.2-21  purrr_0.2.2        kernlab_0.9-25
 [5] reshape2_1.4.1     lattice_0.20-34    colorspace_1.2-7   htmltools_0.3.5
 [9] stats4_3.2.3       viridisLite_0.1.3  yaml_2.1.13        base64enc_0.1-3
[13] DBI_0.5-1          prabclus_2.2-6     RColorBrewer_1.1-2 registry_0.3
[17] fpc_2.1-10         foreach_1.4.3      plyr_1.8.4         robustbase_0.92-6
[21] stringr_1.1.0      munsell_0.4.3      gtable_0.2.0       htmlwidgets_0.7
[25] caTools_1.17.1     mvtnorm_1.0-5      codetools_0.2-15   labeling_0.3
[29] seriation_1.2-1    flexmix_2.3-13     class_7.3-14       DEoptimR_1.0-6
[33] trimcluster_0.1-2  Rcpp_0.12.7        KernSmooth_2.23-15 scales_0.4.1
[37] diptest_0.75-7     gdata_2.17.0       jsonlite_1.1       gplots_3.0.1
[41] gridExtra_2.2.1    digest_0.6.10      gclus_1.3.1        dplyr_0.5.0
[45] grid_3.2.3         tools_3.2.3        bitops_1.0-6       magrittr_1.5
[49] lazyeval_0.2.0     tibble_1.2         cluster_2.0.5      whisker_0.3-2
[53] tidyr_0.6.0        dendextend_1.3.0   MASS_7.3-45        assertthat_0.1
[57] httr_1.2.1         iterators_1.0.8    R6_2.2.0           TSP_1.1-4
[61] mclust_5.2         nnet_7.3-12
talgalili commented 7 years ago

Hi there, I see you are using heatmaply 0.6.0. Please update to the latest on CRAN (0.7.0). This is working fine for me:

image

Please let me know if it doesn't.

Cheers, Tal

talgalili commented 7 years ago

p.s.: consider using the following for an alternative look at your data:

heatmaply(percentize(example_df))

image

bextra commented 7 years ago

Good tip on the percentize. I will update and see how it goes. Thanks!

bextra commented 7 years ago

Hi Tal. I have updated to heatmaply 0.7.0 and can generate the heatmap locally, but on our cluster, I'm still getting the error. Do you have any idea what could be causing that?

Here is the updated sessionInfo of our cluster:

R version 3.2.3 (2015-12-10)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux

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  base     

other attached packages:
 [1] beakR_0.1.3.9000  heatmaply_0.7.0   viridis_0.3.4    
 [4] plotly_4.5.6      scales_0.4.1      htmltools_0.3.5  
 [7] stringr_1.1.0     reshape2_1.4.1    ggplot2_2.2.1    
[10] d3heatmap_0.6.1.1 knitr_1.14       

loaded via a namespace (and not attached):
 [1] gtools_3.5.0       modeltools_0.2-21  purrr_0.2.2       
 [4] kernlab_0.9-25     lattice_0.20-34    colorspace_1.2-7  
 [7] stats4_3.2.3       viridisLite_0.1.3  yaml_2.1.13       
[10] base64enc_0.1-3    DBI_0.5-1          prabclus_2.2-6    
[13] registry_0.3       fpc_2.1-10         foreach_1.4.3     
[16] plyr_1.8.4         robustbase_0.92-6  munsell_0.4.3     
[19] gtable_0.2.0       caTools_1.17.1     htmlwidgets_0.7   
[22] mvtnorm_1.0-5      codetools_0.2-15   evaluate_0.10     
[25] seriation_1.2-1    flexmix_2.3-13     class_7.3-14      
[28] DEoptimR_1.0-6     trimcluster_0.1-2  methods_3.2.3     
[31] Rcpp_0.12.7        KernSmooth_2.23-15 diptest_0.75-7    
[34] formatR_1.4        gdata_2.17.0       jsonlite_1.1      
[37] gplots_3.0.1       gridExtra_2.2.1    png_0.1-7         
[40] digest_0.6.10      gclus_1.3.1        stringi_1.1.2     
[43] dplyr_0.5.0        grid_3.2.3         bitops_1.0-6      
[46] tools_3.2.3        magrittr_1.5       lazyeval_0.2.0    
[49] tibble_1.2         cluster_2.0.5      whisker_0.3-2     
[52] tidyr_0.6.0        dendextend_1.4.0   MASS_7.3-45       
[55] assertthat_0.1     rmarkdown_1.1      httr_1.2.1        
[58] iterators_1.0.8    R6_2.2.0           TSP_1.1-4         
[61] mclust_5.2         nnet_7.3-12
talgalili commented 7 years ago

I'm not sure what to say about that. What code is running in the cluster exactly?