Hello Biostar,
I wish to change the colors of a row annotation on a heatmap. I use ComplexHeatmap and would like to use RColorBrewer for colors which will map a vector with continuous values. I have difficulties to create a list of colors and and to have it map the rows of my mat on the heatmap.
A quick example would be much appreciated.
Best,
Franc
EDIT :
Example code:
set.seed(123)
mat <- data.frame(matrix(rnorm(100), 10), row.names = sample(letters, 10, replace = F))
base <- matrix(abs(rnorm(10,mean=10)), ncol = 1)
rownames(base) <- rownames(mat)
row_annot <- data.frame(Expression = log2(base))
Var <- setNames(hcl.colors(nrow(row_annot),"Heat"), rownames(mat))
row_ha <- HeatmapAnnotation(df = row_annot,
col = list(Expression = Var),
which = "row",
show_annotation_name = F,
annotation_name_side = "top",
annotation_legend_param = list()
)
scaled_mat <- t(scale(t(mat), center = T))
Heatmap(scaled_mat, name = "mat", right_annotation = row_ha)
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] GOSemSim_2.10.0 dplyr_0.8.3 ComplexHeatmap_2.0.0
[4] viridis_0.5.1 viridisLite_0.3.0 PANTHER.db_1.0.4
[7] RSQLite_2.1.2 stringr_1.4.0 colorRamps_2.3
[10] VennDiagram_1.6.20 futile.logger_1.4.3 clusterProfiler_3.12.0
[13] reactome.db_1.68.0 org.Mm.eg.db_3.8.2 ggrepel_0.8.1
[16] data.table_1.12.2 gageData_2.22.0 pathview_1.24.0
[19] org.Hs.eg.db_3.8.2 AnnotationDbi_1.46.1 gage_2.34.0
[22] biomaRt_2.40.4 ggplot2_3.2.1 pheatmap_1.0.12
[25] RColorBrewer_1.1-2 gplots_3.0.1.1 DESeq2_1.24.0
[28] SummarizedExperiment_1.14.1 DelayedArray_0.10.0 BiocParallel_1.18.1
[31] matrixStats_0.55.0 Biobase_2.44.0 GenomicRanges_1.36.1
[34] GenomeInfoDb_1.20.0 IRanges_2.18.2 S4Vectors_0.22.1
[37] BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] circlize_0.4.8 backports_1.1.4 Hmisc_4.2-0
[4] fastmatch_1.1-0 plyr_1.8.4 igraph_1.2.4.1
[7] lazyeval_0.2.2 splines_3.6.1 urltools_1.7.3
[10] digest_0.6.20 htmltools_0.3.6 GO.db_3.8.2
[13] gdata_2.18.0 magrittr_1.5 checkmate_1.9.4
[16] memoise_1.1.0 cluster_2.1.0 Biostrings_2.52.0
[19] annotate_1.62.0 graphlayouts_0.5.0 enrichplot_1.4.0
[22] prettyunits_1.0.2 colorspace_1.4-1 blob_1.2.0
[25] xfun_0.9 crayon_1.3.4 RCurl_1.95-4.12
[28] jsonlite_1.6 graph_1.62.0 genefilter_1.66.0
[31] zeallot_0.1.0 survival_2.44-1.1 glue_1.3.1
[34] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.30.0
[37] XVector_0.24.0 UpSetR_1.4.0 GetoptLong_0.1.7
[40] Rgraphviz_2.28.0 shape_1.4.4 scales_1.0.0
[43] DOSE_3.10.2 futile.options_1.0.1 DBI_1.0.0
[46] Rcpp_1.0.2 xtable_1.8-4 progress_1.2.2
[49] htmlTable_1.13.1 clue_0.3-57 gridGraphics_0.4-1
[52] foreign_0.8-72 bit_1.1-14 europepmc_0.3
[55] Formula_1.2-3 htmlwidgets_1.3 httr_1.4.1
[58] fgsea_1.10.1 acepack_1.4.1 pkgconfig_2.0.2
[61] XML_3.98-1.20 farver_1.1.0 nnet_7.3-12
[64] locfit_1.5-9.1 labeling_0.3 ggplotify_0.0.4
[67] tidyselect_0.2.5 rlang_0.4.0 reshape2_1.4.3
[70] munsell_0.5.0 tools_3.6.1 ggridges_0.5.1
[73] knitr_1.24 bit64_0.9-7 tidygraph_1.1.2
[76] caTools_1.17.1.2 purrr_0.3.2 KEGGREST_1.24.0
[79] ggraph_2.0.0 formatR_1.7 KEGGgraph_1.44.0
[82] DO.db_2.9 xml2_1.2.2 compiler_3.6.1
[85] rstudioapi_0.10 curl_4.0 png_0.1-7
[88] tibble_2.1.3 tweenr_1.0.1 geneplotter_1.62.0
[91] stringi_1.4.3 lattice_0.20-38 Matrix_1.2-17
[94] vctrs_0.2.0 pillar_1.4.2 lifecycle_0.1.0
[97] BiocManager_1.30.4 GlobalOptions_0.1.0 triebeard_0.3.0
[100] cowplot_1.0.0 bitops_1.0-6 qvalue_2.16.0
[103] R6_2.4.0 latticeExtra_0.6-28 KernSmooth_2.23-15
[106] gridExtra_2.3 lambda.r_1.2.3 MASS_7.3-51.4
[109] gtools_3.8.1 assertthat_0.2.1 rjson_0.2.20
[112] withr_2.1.2 GenomeInfoDbData_1.2.1 hms_0.5.1
[115] rpart_4.1-15 tidyr_1.0.0 rvcheck_0.1.3
[118] ggforce_0.3.1 base64enc_0.1-3
•
written
by
fmarchildo •
Thanks again for your patience and help RamRS. Got my answer here: https://github.com/jokergoo/ComplexHeatmap/issues/359#issuecomment-531669275
Appreciate the update but please mention (or even better, avoid) cross-posting in the future. It annoys people in multiple communities.
Ideally, your question belonged on Bioconductor support as you’re seeking help with a Bioconductor package. We here are ok dealing with those questions too. GitHub is not the place to ask questions - it is for filing genuine bug reports and contributing to the source code.
Thanks RamRS. I will be sure to post my future inquiries to the best group.
Thanks for your help RamRS. I think that wouldn't work because the col argument of HeatmapAnnotation requires a named list of color not a vector.
set.seed(123)
mat <- data.frame(matrix(rnorm(100), 10), row.names = sample(letters, 10, replace = F))
base <- matrix(abs(rnorm(10,mean=10)), ncol = 1)
rownames(base) <- rownames(mat)
row_annot <- data.frame(Expression = log2(base))
Var <- setNames(hcl.colors(nrow(row_annot),"Heat"), rownames(mat))
row_ha <- HeatmapAnnotation(df = row_annot,
col = list(Expression = Var),
which = "row",
show_annotation_name = F,
annotation_name_side = "top",
annotation_legend_param = list()
)
scaled_mat <- t(scale(t(mat), center = T))
Heatmap(scaled_mat, name = "mat", right_annotation = row_ha)
R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base
other attached packages:
[1] GOSemSim_2.10.0 dplyr_0.8.3 ComplexHeatmap_2.0.0
[4] viridis_0.5.1 viridisLite_0.3.0 PANTHER.db_1.0.4
[7] RSQLite_2.1.2 stringr_1.4.0 colorRamps_2.3
[10] VennDiagram_1.6.20 futile.logger_1.4.3 clusterProfiler_3.12.0
[13] reactome.db_1.68.0 org.Mm.eg.db_3.8.2 ggrepel_0.8.1
[16] data.table_1.12.2 gageData_2.22.0 pathview_1.24.0
[19] org.Hs.eg.db_3.8.2 AnnotationDbi_1.46.1 gage_2.34.0
[22] biomaRt_2.40.4 ggplot2_3.2.1 pheatmap_1.0.12
[25] RColorBrewer_1.1-2 gplots_3.0.1.1 DESeq2_1.24.0
[28] SummarizedExperiment_1.14.1 DelayedArray_0.10.0 BiocParallel_1.18.1
[31] matrixStats_0.55.0 Biobase_2.44.0 GenomicRanges_1.36.1
[34] GenomeInfoDb_1.20.0 IRanges_2.18.2 S4Vectors_0.22.1
[37] BiocGenerics_0.30.0
loaded via a namespace (and not attached):
[1] circlize_0.4.8 backports_1.1.4 Hmisc_4.2-0
[4] fastmatch_1.1-0 plyr_1.8.4 igraph_1.2.4.1
[7] lazyeval_0.2.2 splines_3.6.1 urltools_1.7.3
[10] digest_0.6.20 htmltools_0.3.6 GO.db_3.8.2
[13] gdata_2.18.0 magrittr_1.5 checkmate_1.9.4
[16] memoise_1.1.0 cluster_2.1.0 Biostrings_2.52.0
[19] annotate_1.62.0 graphlayouts_0.5.0 enrichplot_1.4.0
[22] prettyunits_1.0.2 colorspace_1.4-1 blob_1.2.0
[25] xfun_0.9 crayon_1.3.4 RCurl_1.95-4.12
[28] jsonlite_1.6 graph_1.62.0 genefilter_1.66.0
[31] zeallot_0.1.0 survival_2.44-1.1 glue_1.3.1
[34] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.30.0
[37] XVector_0.24.0 UpSetR_1.4.0 GetoptLong_0.1.7
[40] Rgraphviz_2.28.0 shape_1.4.4 scales_1.0.0
[43] DOSE_3.10.2 futile.options_1.0.1 DBI_1.0.0
[46] Rcpp_1.0.2 xtable_1.8-4 progress_1.2.2
[49] htmlTable_1.13.1 clue_0.3-57 gridGraphics_0.4-1
[52] foreign_0.8-72 bit_1.1-14 europepmc_0.3
[55] Formula_1.2-3 htmlwidgets_1.3 httr_1.4.1
[58] fgsea_1.10.1 acepack_1.4.1 pkgconfig_2.0.2
[61] XML_3.98-1.20 farver_1.1.0 nnet_7.3-12
[64] locfit_1.5-9.1 labeling_0.3 ggplotify_0.0.4
[67] tidyselect_0.2.5 rlang_0.4.0 reshape2_1.4.3
[70] munsell_0.5.0 tools_3.6.1 ggridges_0.5.1
[73] knitr_1.24 bit64_0.9-7 tidygraph_1.1.2
[76] caTools_1.17.1.2 purrr_0.3.2 KEGGREST_1.24.0
[79] ggraph_2.0.0 formatR_1.7 KEGGgraph_1.44.0
[82] DO.db_2.9 xml2_1.2.2 compiler_3.6.1
[85] rstudioapi_0.10 curl_4.0 png_0.1-7
[88] tibble_2.1.3 tweenr_1.0.1 geneplotter_1.62.0
[91] stringi_1.4.3 lattice_0.20-38 Matrix_1.2-17
[94] vctrs_0.2.0 pillar_1.4.2 lifecycle_0.1.0
[97] BiocManager_1.30.4 GlobalOptions_0.1.0 triebeard_0.3.0
[100] cowplot_1.0.0 bitops_1.0-6 qvalue_2.16.0
[103] R6_2.4.0 latticeExtra_0.6-28 KernSmooth_2.23-15
[106] gridExtra_2.3 lambda.r_1.2.3 MASS_7.3-51.4
[109] gtools_3.8.1 assertthat_0.2.1 rjson_0.2.20
[112] withr_2.1.2 GenomeInfoDbData_1.2.1 hms_0.5.1
[115] rpart_4.1-15 tidyr_1.0.0 rvcheck_0.1.3
[118] ggforce_0.3.1 base64enc_0.1-3
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You could pass in a vector of colors to the
colparameter. See: https://jokergoo.github.io/ComplexHeatmap-reference/book/heatmap-annotations.html#simple-annotationshould give you 9 colors, for example. If you need more colors than any of RColorBrewer's palettes can offer you, you can either use colorRamp* functions to interpolate colors (only makes sense for continuous/sequential values) or choose a different color package. See here on more information about interpolating colors.
Thanks for your help RamRS. I think that wouldn't work because the col argument of HeatmapAnnotation requires a named list of color not a vector.
There exists a function called
setNamesthat can be helpful here:Of course, you can also get a named
listinstead of a namedvector:Thanks RamRS. Sure but then, I have many more than 7 rows.
That was an example - it can be expanded to as many elements as you need. All that matters is that the first and second arguments have the same length (excluding possible special cases).
Yes I see. Nevertheless, I think the HeatmapAnnotation method has a bug because upon testing your example, I get the following error: Error: elements in
colshould be named vectors.Can you please paste your code so we can have a look at what's going on?
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