Author: Joe Cheng and Tal Galili
Date: 2016-02-23

# Introduction to d3heatmap

#### Joe Cheng and Tal Galili

#### 2016-02-23

# Exampels

    suppressMessages(library(dendextend))
    library(d3heatmap)

## mtcars

    x <- mtcars # [c(2:4,7),1:4]

    d3heatmap(x, k_row = 4, k_col = 2)

    ## Loading required namespace: colorspace

    d3heatmap(x, k_row = 4, k_col = 2, scale = "column") # a more appropriate scalling

    # row_dend2 <- x %>% dist %>% hclust %>% as.dendrogram %>%
    #   color_branches(k = 3)
    # col_dend2 <- x %>% t %>% dist %>% hclust %>% as.dendrogram %>%
    #   color_branches(k = 2)
    # d3heatmap(x, Rowv = row_dend2, Colv = col_dend2)
    # d3heatmap(x, Rowv = row_dend2, Colv = col_dend2, scale = "column") # a more appropriate scaling

We can also look at the correlation between the measures:

    x_cor <- cor(x)

    x_cor %>% d3heatmap(k_row = 3, k_col = 3) # (symm = TRUE)

    # x_cor %>% d3heatmap(reorderfun = function(x, ...) x) # this doesn't reorder the rows/columns based on the means.
    # Note the use of k_row/k_col to color the branches

    # # reproducing the dendrogram, but with manually created the dendrograms
    # cor_dend <- x_cor  %>% dist %>% hclust(method = "com") %>% as.dendrogram %>%
    #   color_branches(k = 3) %>%
    #   reorder(rowMeans(x_cor)) # this is what is done inside heatmap.
    # x_cor %>% d3heatmap(Rowv = cor_dend, Colv = cor_dend)

## Iris

    x <- datasets::iris[,-5] # [c(2:4,7),1:4]

    row_dend2 <- x %>% dist %>% hclust(method = "ave") %>% as.dendrogram %>%
      color_branches(k = 3) %>%
      reorder(rowMeans(x))
    col_dend2 <- x %>% t %>% dist %>% hclust %>% as.dendrogram %>%
      color_branches(k = 2) %>%
      sort # This sorting requires dendextend and cannot be easily done without it

    d3heatmap(x, Rowv = row_dend2, Colv = col_dend2,
              colors = "Greens",
              # scale = "row",
              width = 600,
              show_grid = FALSE)

# Session info

    sessionInfo()

    ## R version 3.2.2 (2015-08-14)
    ## Platform: x86_64-apple-darwin13.4.0 (64-bit)
    ## Running under: OS X 10.11.3 (El Capitan)
    ##
    ## locale:
    ## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] d3heatmap_0.6.1.1 dendextend_1.0.1
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] Rcpp_0.12.3        png_0.1-7          digest_0.6.9
    ##  [4] plyr_1.8.3         jsonlite_0.9.19    formatR_1.2.1
    ##  [7] magrittr_1.5       scales_0.3.0       evaluate_0.8
    ## [10] stringi_1.0-1      whisker_0.3-2      rmarkdown_0.9.2
    ## [13] RColorBrewer_1.1-2 tools_3.2.2        stringr_1.0.0
    ## [16] htmlwidgets_0.6    munsell_0.4.2      yaml_2.1.13
    ## [19] colorspace_1.2-6   base64enc_0.1-3    htmltools_0.3.2
    ## [22] knitr_1.12.3