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How to make a heatmap showing signatures of scores from 0 to 1 in R?

Hi,

I have a data matrix mat of 622 samples as columns and cell types as rows. 

sample annotation:

Samples      Group
Sample1         A   
Sample2         A
Sample3         A
Sample4         A
Sample5         B
Sample6         B
Sample7         B
Sample8         B

Here I am showing a small example data which looks like below: 

             Sample1    Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8
Adipocytes      0          0       0       0     0.003  2.00E-04   0       0
Astrocytes      0          0       0    0.1343  0.1011  0.0562  0.0791  0.0089
B-cells.    0.0095      0.0059  0.0378  0.0016    0     0.0673  0.0361  0.0468
Basophils   0.0091      0.0229     0    0.0864    0     0.069   0.026   0.0994
CD4+ T-cells    0          0       0       0      0        0       0       0
CD4+ Tcm        0          0    0.013   0.0401  0.0053     0    0.0362     0
CD4+ Tem        0      0.0382   0.0268  0.0372    0        0    0.0451  0.0729
CD4+ m T-cells  0.046   0.027   0.0229     0    0.0109  0.0278     0    0.0258
CD4+ n T-cells  0          0       0       0      0     0.0037  0.0196     0
CD8+ T-cells    0.0195 5.00E-04 0.0198     0      0     0.0297  0.0036  0.0646
CD8+ Tcm    0.0108         0       0       0      0     0.0475     0    0.0746
CD8+ Tem        0          0       0       0      0     0.0012  0.0038  0.0483
CD8+ n T-cells  0.0216  0.0027  0.0124     0    0.0055  0.014      0    0.0132

I am using complex heatmap to generate heatmap showing signatures.

I tried like below, but I have an error:

ann <- data.frame(samples$Group)
colnames(ann) <- c("Type")
colours <- list("Type"=c("A"="orange","B"="darkgreen"))
colAnn <- HeatmapAnnotation(df=ann, which="col", col=colours, annotation_width=unit(c(1, 4), "cm"), gap=unit(1, "mm"))

myCol <- colorRampPalette(c("navyblue", "#002bff"))(100)
myBreaks <- seq(-1,1, length=100)
hmap <- Heatmap(mat, name = "xCell scores", col = colorRamp2(myBreaks, myCol),
                width = unit(100, "mm"),show_row_names = TRUE, show_column_names = FALSE, cluster_rows = FALSE,
                cluster_columns = FALSE, show_column_dend = FALSE, show_row_dend = FALSE,
                row_dend_reorder = FALSE, column_dend_reorder = FALSE)
draw(hmap, heatmap_legend_side="left", annotation_legend_side="right")

The Error I got:

Error in labels_mat[, i] : subscript out of bounds
In addition: Warning message:
In matrix(1:(nrow * ncol), nrow = nrow, ncol = ncol, byrow = by_row) :
  data length exceeds size of matrix

I want to plot to be looked like this which is from Figure 2a in this paperenter image description here

Any help is appreciated. thanq

rna-seq heatmap complexheatmap r signatures
• 3,512 views • link
written by newbie newbie
  • Your draw specifies an annotation_legend_side, but you don't have any annotations. What's going on there?
  • cluster_rows=FALSE and clustering_method_rows="ward.D2": Why do you have a clustering method when clustering is disabled?
• 0 views • link
written by Ram Ram

sorry that was a mistake. there is no annotation_legend_side I removed that in question.

• 0 views • link
written by newbie newbie

What are the output to dim(mat) and class(mat)? Can you also paste the output of sessionInfo()?

• 0 views • link
written by Ram Ram 
dim(mat)
67 622

class(mat)
matrix

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

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

attached base packages:
 [1] parallel  stats4    grid      stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] fgsea_1.10.0           Rcpp_1.0.1             ReactomePA_1.28.0     
 [4] org.Hs.eg.db_3.8.2     AnnotationDbi_1.46.0   IRanges_2.18.1        
 [7] S4Vectors_0.22.0       Biobase_2.44.0         BiocGenerics_0.30.0   
[10] clusterProfiler_3.12.0 forcats_0.4.0          stringr_1.4.0         
[13] dplyr_0.8.1            purrr_0.3.2            readr_1.3.1           
[16] tidyr_0.8.3            tibble_2.1.3           ggplot2_3.1.1         
[19] tidyverse_1.2.1        RColorBrewer_1.1-2     circlize_0.4.6        
[22] ComplexHeatmap_2.0.0   gplots_3.0.1.1         matrixStats_0.54.0    
[25] edgeR_3.26.4           limma_3.40.2          

loaded via a namespace (and not attached):
 [1] colorspace_1.4-1    rjson_0.2.20        ellipsis_0.1.0      ggridges_0.5.1     
 [5] qvalue_2.16.0       GlobalOptions_0.1.0 clue_0.3-57         rstudioapi_0.10    
 [9] farver_1.1.0        urltools_1.7.3      ggrepel_0.8.1       bit64_0.9-7        
[13] lubridate_1.7.4     xml2_1.2.0          splines_3.6.0       GOSemSim_2.10.0    
[17] polyclip_1.10-0     jsonlite_1.6        broom_0.5.2         cluster_2.0.9      
[21] GO.db_3.8.2         png_0.1-7           graph_1.62.0        graphite_1.30.0    
[25] ggforce_0.2.2       compiler_3.6.0      httr_1.4.0          rvcheck_0.1.3      
[29] backports_1.1.4     assertthat_0.2.1    Matrix_1.2-17       lazyeval_0.2.2     
[33] cli_1.1.0           tweenr_1.0.1        prettyunits_1.0.2   tools_3.6.0        
[37] igraph_1.2.4.1      gtable_0.3.0        glue_1.3.1          reshape2_1.4.3     
[41] DO.db_2.9           rappdirs_0.3.1      fastmatch_1.1-0     enrichplot_1.4.0   
[45] cellranger_1.1.0    gdata_2.18.0        nlme_3.1-140        ggraph_1.0.2       
[49] rvest_0.3.4         gtools_3.8.1        statmod_1.4.32      DOSE_3.10.1        
[53] europepmc_0.3       MASS_7.3-51.4       scales_1.0.0        reactome.db_1.68.0 
[57] hms_0.4.2           yaml_2.2.0          memoise_1.1.0       gridExtra_2.3      
[61] UpSetR_1.4.0        triebeard_0.3.0     stringi_1.4.3       RSQLite_2.1.1      
[65] checkmate_1.9.3     caTools_1.17.1.2    BiocParallel_1.18.0 shape_1.4.4        
[69] rlang_0.3.4         pkgconfig_2.0.2     bitops_1.0-6        lattice_0.20-38    
[73] labeling_0.3        cowplot_0.9.4       bit_1.1-14          tidyselect_0.2.5   
[77] plyr_1.8.4          magrittr_1.5        R6_2.4.0            generics_0.0.2     
[81] DBI_1.0.0           pillar_1.4.1        haven_2.1.0         withr_2.1.2        
[85] modelr_0.1.4        crayon_1.3.4        KernSmooth_2.23-15  viridis_0.5.1      
[89] GetoptLong_0.1.7    progress_1.2.2      locfit_1.5-9.1      readxl_1.3.1       
[93] data.table_1.12.2   blob_1.1.1          digest_0.6.19       gridGraphics_0.4-1 
[97] munsell_0.5.0       viridisLite_0.3.0   ggplotify_0.0.3
• 0 views • link
written by newbie newbie

Switch to github latest version of ComplexHeatmap: devtools::install_github('jokergoo/ComplexHeatmap'). If already installed through github, please use devtools::update_packages() and pick the number displayed against ComplexHeatmap. It's a rapidly evolving package and you are quite a few versions behind.

• 0 views • link
written by Ram Ram

sure I will. But may I know something about the error and how to make a plot like above please

• 0 views • link
written by newbie newbie

Try updating and see if the error persists. If it does and the error is the same, we can work on figuring out what's happening.

• 0 views • link
written by Ram Ram

Yes, I did that and I see the same error again.

• 0 views • link
written by newbie newbie

Can you check your sessionInfo() to be sure you're using ComplexHeatmap v 2.1.0? Your matrix looks fine, you should not be seeing this error.

If you're using the right version, try this:

mat.tmp <- mat
rownames(mat.tmp) <- NULL
hmap.tmp <- Heatmap(mat.tmp, name = "xCell scores", col = colorRamp2(myBreaks, myCol),
            width = unit(100, "mm"),show_row_names = TRUE, show_column_names = FALSE, cluster_rows = FALSE,
            cluster_columns = FALSE, show_column_dend = FALSE, show_row_dend = FALSE,
            row_dend_reorder = FALSE, column_dend_reorder = FALSE)
draw(hmap.tmp)

Also, try modifying the 100 in the colorRampPalette(c("navyblue", "#002bff"))(100) to 42000.

• 0 views • link
written by Ram Ram

sorry, there is no change in the error. And in my question I also added the sample annotation now and will be using annotation_legend_side argument now.

The error still says same. 

Error in labels_mat[, i] : subscript out of bounds
In addition: Warning message:
In matrix(1:(nrow * ncol), nrow = nrow, ncol = ncol, byrow = by_row) :
  data length exceeds size of matrix
• 0 views • link
written by newbie newbie

1 answer

For the moment, omit the annotation as it only adds more variables to the problem. Try skipping the col= parameter. Next, just do a simple draw(Heatmap(mat)), see if the error persists. Add options one by one and see when the code breaks. That'll give you a lead to follow.

• 0 views • link
written by Ram Ram

Ok. everything works now. But would like to know how I can bring the samples with values > 0 all together like in the plot given in the question.

In the above image you can see if it is 0 it is light white color and all the samples with values > 0 to 1 were all together for all the cell types. How to get that?

• 0 views • link
written by newbie newbie

You'd either have to cluster the columns or do some sort of guided ordering. I'm not sure how to get to that exact picture.

• 0 views • link
written by Ram Ram

ok np. will have a look. Thanks a lot.

• 0 views • link
written by newbie newbie

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