Heatmap - species clustering by phylogeny
In CALANGO: Comparative Analysis with Annotation-Based Genomic Components

###Prepare data.frame to plot

##getting data frame linking genome IDs to groups and short names
mynames <- data.frame(genomeID  = defs$y.name, 
                      group     = defs$groups, 
                      shortName = defs$short.name)

##DEBUG
#y.name
#groups
#short.name
#names


##getting relevant annotation IDs to plot only them
ids <- as.vector(defs$sig_IDs)

##DEBUG
#ids

#getting annotation frequencies for annotation IDs
tmp <- defs$y[as.vector(ids)]
#tmp <- data.frame(sapply(defs$y[as.vector(ids)], function(x) ifelse(x > 0, 1, 0)))
#mynorm <- tmp
mynorm <- tmp / defs$denominator
rm(tmp)

#replacing genome IDs by user-defined names
rownames(mynorm) <- mynames$shortName[match(rownames(mynorm), mynames$genomeID)]


##DEBUG
#mynorm

#getting a heatmaply-compatible tree

tree <- defs$tree

#replacing genome IDs by short names
tree$tip.label <- mynames$shortName[match(tree$tip.label, mynames$genomeID)]

#2char
tree$tip.label <- sapply(tree$tip.label, function(x) as.character(x))

#final tree must be a dendrogram and a dendextend object
tree2 <- stats::as.dendrogram(ape::as.hclust.phylo(tree))#stats::as.dendrogram(ape::as.phylo(tree))
tree_final <- dendextend::set(tree2, what = "branches_lwd", value = 0.4)

##DEBUG
#plot(tree2)

#colnames(mynorm) <- paste0(ids, " - ", output$annotation.cor[ids])

mat     <- as.matrix(mynorm)
ord.mat <- mat[tree$tip.label, ]
rm(mynorm)

#to create custom hover text by adding annotation definition
onmouseover <- as.data.frame(ord.mat)
onmouseover[] <- lapply(colnames(onmouseover), 
                        function(colname) {
                          paste0("definition: ", 
                                 defs$annotation.cor[colname], "\n")})

##DEBUG
#ord.mat

#color pallete for heatmap
my_palette <- grDevices::colorRampPalette(c("white", "blue"))(n = 51)

#establishing colors for groups
jColors <- data.frame(LABEL = levels(as.factor(mynames$group)),
                      COLOR = I(CALANGO_brewer_pal(nlevels(as.factor(mynames$group)), 
                                                   name = 'Set1')))

##DEBUG
#jColors

#coloring species by group color
tmp       <- data.frame(species = rownames(ord.mat), stringsAsFactors = FALSE)
tmp$group <- mynames$group[match(tmp$species, mynames$shortName)]
tmp$COLOR <- jColors$COLOR[match(tmp$group, jColors$LABEL)]

species2color <- base::unique(tmp[, -2])
species2group <- base::unique(tmp[, -3])
#rm(tmp)

##DEBUG
#species2color

#quantile normalization
#tmp <- normalize.quantiles(as.matrix(ord.mat))
#colnames(tmp) <- colnames(ord.mat)
#rownames(tmp) <- rownames(ord.mat)
#ord.norm.mat <- tmp
#rm(tmp)

#computing distance for row clustering
distance2 <- stats::dist(as.matrix(t(heatmaply::normalize(as.data.frame(ord.mat)))), 
                         method = "euclidean")
cluster2 <- stats::hclust(distance2, method = "average")
#cluster2_final = dendextend::set(as.dendrogram(hclust(distance2, method=c("average"))), "branches_lwd", 0.4)

##DEBUG
#plot(cluster2_final)


#plot(tree_final)

#Plot

#mynorm

mp <- heatmaply::heatmaply(
  t(heatmaply::normalize(as.data.frame(ord.mat))),
  # row_dend_left = TRUE,
  # cexCol = 0.8,
  # subplot_heights=c(0.05, 0.01, 0.94),
  Rowv = cluster2,
  # col_side_colors = NULL,
  # row_side_colors = species2group$group,
  Colv = tree2,
  col = my_palette,
  plot_method= "ggplot",
  custom_hovertext = t(onmouseover),
  subplot_widths=c(0.9, 0.1),
  subplot_heights=c(0.08, 0.02, 0.90),
  col_side_colors = data.frame("Groups" = species2group$group,
                               check.names=FALSE))

suppressWarnings(
  plotly::layout(mp,
                 width  = 25 * nrow(ord.mat), 
                 height = 20 * ncol(ord.mat))
)

#                     code used to generate pdf plots for article
#                     Colv = tree_final,
#                     file="heatmap_norm.pdf",
#                     Rowv = cluster2,
#                     branches_lwd = 0.4,
#                     col = my_palette,
#                     row_dend_left = TRUE,
#                     plot_method= "ggplot",
#                     cexRow = 0.6,
#                    width = 1000,
#                    height = 1000,
#                     custom_hovertext = t(onmouseover),
#                     subplot_widths=c(0.9, 0.1),
#                     subplot_heights=c(0.08, 0.02, 0.90),
#                    k_row = NA,
#                     showticklabels = FALSE,
#                     subplot_heights=c(0.05, 0.01, 0.94),
#                     col_side_colors = NULL,
#                     row_side_colors = species2group$group,
#                     col_side_colors = data.frame("Groups" = species2group$group, check.names=FALSE)
#                     ) %>% plotly::layout(width=25*(nrow(ord.mat)), height=20*(ncol(ord.mat)))