#Data cleaning----
library(tidyverse)

library(pheatmap)


bean_fpkm <- read_table("fpkm_mean.txt")


conditions <- read_csv("samples_description.csv")

cladevb <- c("Phvul.001G112900", "Phvul.001G112800", "Phvul.003G143100", "Phvul.001G112500",
             "Phvul.001G112400", "Phvul.006G037000", "Phvul.002G025600", "Phvul.005G098300",
             "Phvul.005G097900", "Phvul.005G0986002", "Phvul.005G0988000")

exp_cladevb <- bean_fpkm %>%
  dplyr::filter(gene %in% cladevb) 


hhht_all_tissues <- exp_cladevb %>%
  dplyr::filter(gene == "Phvul.006G037000") %>%
  dplyr::select(-gene) %>%
  pivot_longer(cols= everything(),
               names_to = "sample",
               values_to = "expression") 

hhht_all_tissues <- hhht_all_tissues %>% 
  dplyr::left_join(conditions, by = "sample")


matrix <- hhht_all_tissues %>%
  dplyr::select(-sample) %>%
  pivot_wider(names_from = name,
              values_from = expression)

h <- as.matrix(matrix)
#heatmap---
#Overwrite default draw_colnames in the pheatmap package.
# Thanks to Josh O'Brien at http://stackoverflow.com/questions/15505607
draw_colnames_45 <- function (coln, gaps, ...) {
  coord <- pheatmap:::find_coordinates(length(coln), gaps)
  x     <- coord$coord - 0.5 * coord$size
  res   <- grid::textGrob(
    coln, x = x, y = unit(1, "npc") - unit(3,"bigpts"),
    vjust = 0.75, hjust = 1, rot = 60, gp = grid::gpar(...)
  )
  return(res)
}
assignInNamespace(
  x = "draw_colnames",
  value = "draw_colnames_45",
  ns = asNamespace("pheatmap")
)
#Colors ----

mypalette<- colorRampPalette(c("#FFFFFF","#6C9CBC","#4C91BD","#0768A7"))(n = 299)

#Exporting image ----
cairo_ps("final_heatmap",
         width = 7.5,
         height = 5)
pheatmap (h,
          main="hhht expression data",
          cellwidth=19,
          cellheight=17,
          display_numbers = TRUE,
          number_format = "%.1f",
          number_color = "black",
          border_color ="grey", #square edges color
          clustering_distance_cols="euclidean",
          treeheight_row=75, #dendogram height, default is 50
          clustering_method="complete",
          cluster_cols=TRUE,
          cluster_rows=FALSE,
          fontsize=7.8,
          col = mypalette,
          margins=c(5,10))
dev.off()