Hi,

I am using dendextend to plot hclust tree objects generated by each hclust method from hclust{stats}: "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).

I notice the color coding for color_branches fails when I use method = "median" or "centroid".

I tested it with randomly generated matrix and error is replicated for the "median" and "centroid" methods, is there a specific reason for this?

set.seed(1)
df <- as.data.frame(replicate(10, rnorm(20)))
df.names <- rep(c("black", "red", "blue", "green", "cyan"), 2)
df.col <- rep(c("black", "red", "blue", "green", "cyan"), 2)
colnames(df) <- df.names
df.dist <- dist(t(df), method = "euclidean")

# plotting works for "ward.D", "ward.D2", "single", "complete", "average", "mcquitty"
dend <- as.dendrogram(hclust(df.dist, method = "ward.D2"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

# color_branches fails for "median" or "centroid"
dend <- as.dendrogram(hclust(df.dist, method = "median"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

dend <- as.dendrogram(hclust(df.dist, method = "centroid"), labels = df.names)
labels_colors(dend) <- df.col[order.dendrogram(dend)]
dend.colorBranch <- color_branches(dend, k = length(df.names), col = df.col[order.dendrogram(dend)])
dend.colorBranch %>% set("branches_lwd", 3) %>% plot(horiz = TRUE)

Session Info below:

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

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  methods   base 

other attached packages:
 [1] hexbin_1.27.1              vsn_3.42.3                 DESeq2_1.14.1              SummarizedExperiment_1.4.0 BiocParallel_1.8.1        
 [6] arrayQualityMetrics_3.30.0 UniProt.ws_2.14.0          RCurl_1.95-4.8             bitops_1.0-6               RSQLite_1.1-2             
[11] HGNChelper_0.3.4           biomaRt_2.30.0             EnsDb.Hsapiens.v75_2.1.0   ensembldb_1.6.2            GenomicFeatures_1.26.2    
[16] GenomicRanges_1.26.2       GenomeInfoDb_1.10.3        org.Hs.eg.db_3.4.0         AnnotationDbi_1.36.2       IRanges_2.8.1             
[21] S4Vectors_0.12.1           Biobase_2.34.0             BiocGenerics_0.20.0        factoextra_1.0.4.999       FactoMineR_1.35           
[26] ggbiplot_0.55              scales_0.4.1               plyr_1.8.4                 devtools_1.12.0            calibrate_1.7.2           
[31] MASS_7.3-45                cluster_2.0.5              squash_1.0.7               ggdendro_0.1-20            xlsx_0.5.7                
[36] xlsxjars_0.6.1             rJava_0.9-8                gridExtra_2.2.1            dendextend_1.4.0           ggrepel_0.6.5             
[41] ggplot2_2.2.1              pheatmap_1.0.8             lattice_0.20-34            RColorBrewer_1.1-2         gplots_3.0.1              
[46] reshape2_1.4.2             reshape_0.8.6              tidyr_0.6.1                dplyr_0.5.0                circlize_0.3.9            
[51] migest_1.7.3