R/wordcloud_heatmap.R

In neurogenomics/scNLP: NLP for Single-cell Omics.

# 
# wordcloud_heatmap <- function(mnn_list){
#   
#   
#   source("https://gist.githubusercontent.com/jokergoo/bfb115200df256eeacb7af302d4e508e/raw/14f315c7418f3458d932ad749850fd515dec413b/word_cloud_grob.R")
#   
#   ht <- Heatmap(mat, 
#                 name = "mat",
#                 show_row_names = F,
#                 show_column_names = F,
#                 top_annotation = column_ha,
#                 left_annotation = row_ha,
#                 row_km = mnn_list$metadata$cluster,
#                 column_km = mnn_list$metadata$cluster)
#   
#   clusts <- cbind(mnn_list$metadata, mnn_list$reduction_coords)
#   tfidf.celltype <- tf_idf(clusts, "celltype", terms_per_cluster = 2)
#   keywords <- lapply(unique(tfidf.celltype$cluster), function(x){
#     dat <- data.frame(tfidf.celltype[tfidf.celltype$cluster==x,])
#     row.names(dat) <- dat$word
#     return(dat)
#   }) |> `names<-`(unique(tfidf.celltype$cluster))
#   
#   align_to = split(seq_len(nrow(mat)), mnn_list$metadata$cluster)
#   # align_to = align_to[names(align_to) != "0"]
#   align_to = align_to[names(align_to) %in% names(keywords)]
#   # align_to
#   
#   
#   fontsize_range = c(4, 16)
#   gbl = lapply(names(align_to), function(nm) {
#     kw = keywords[[nm]][, 1]
#     freq = keywords[[nm]][, 2]
#     fontsize = keywords[[nm]]$tf_idf
#     # scale_fontsize(freq, rg = c(1, max(10, freq)), fs = fontsize_range)
#     word_cloud_grob(text = kw, fontsize = fontsize)
#   })
#   names(gbl) = names(align_to)
#   # gbl
#   
#   margin = unit(8, "pt")
#   gbl_h = lapply(gbl, function(x) convertHeight(grobHeight(x), "cm") + margin)
#   gbl_h = do.call(unit.c, gbl_h)
#   
#   gbl_w = lapply(gbl, function(x) convertWidth(grobWidth(x), "cm"))
#   gbl_w = do.call(unit.c, gbl_w)
#   gbl_w = max(gbl_w) + margin
#   
#   panel_fun = function(index, nm) {
#     # background
#     grid.rect(gp = gpar(fill = "#DDDDDD", col = NA))
#     # border
#     grid.lines(c(0, 1, 1, 0), c(0, 0, 1, 1), gp = gpar(col = "#AAAAAA"), 
#                default.units = "npc")
#     gb = gbl[[nm]]
#     # a viewport within the margins
#     pushViewport(viewport(x = margin/2, y = margin/2, 
#                           width = grobWidth(gb), height = grobHeight(gb),
#                           just = c("left", "bottom")))
#     grid.draw(gb)
#     popViewport()
#   }
#   
#   ht = ht + rowAnnotation(keywords = anno_link(align_to = align_to, 
#                                                which = "row", panel_fun = panel_fun, 
#                                                size = gbl_h, gap = unit(2, "mm"), 
#                                                width = gbl_w + unit(5, "mm"), # 5mm for the link
#                                                link_gp = gpar(fill = "#DDDDDD", col = "#AAAAAA"), 
#                                                internal_line = FALSE)) # you can set it to TRUE to see what happens
#   draw(ht, ht_gap = unit(2, "pt"))
# }
# 
#