############################
### CREATE EMBEDSOM PLOT ###
############################

#you might need this:
#devtools::install_github('exaexa/EmbedSOM')

set.seed(1234)

# run FlowSOM (initial steps prior to meta-clustering)
out <- FlowSOM::ReadInput(data_FlowSOM, transform = FALSE, scale = FALSE)
out <- FlowSOM::BuildSOM(out)

esom <- EmbedSOM::EmbedSOM(out, smooth=1,k=20)

# load cluster labels (if not still loaded)
labels <- paste(raw_data,"_cluster.txt")
#data_labels <- read.table(file_labels, header = TRUE, sep = "\t", stringsAsFactors = FALSE)

labels <- r_data[, "cluster"]


data_plot <- data.frame(EmbedSOM1=esom[,1], EmbedSOM2=esom[,2], Cluster=labels)

ggsave("embedsom.png", dpi=100,
ggplot(data_plot, aes(x = EmbedSOM1, y = EmbedSOM2, color = Cluster)) +
  geom_point(aes(colour = as.factor(labels)),
             size = .5, alpha=.3) +
  scale_color_manual(name = "Cluster",
                     values = c("1" = "#F8766D",
                                "2" = "#CD9600",
                                "3" = "#7CAE00",
                                "4" = "#00BE67",
                                "5" = "#00BFC4",
                                "6" = "#00A9FF",
                                "7" = "#C77CFF",
                                "8" = "#FF61CC")) +
  guides(colour = guide_legend(override.aes = list(size=5))) +
  coord_fixed(ratio = 1) +
  ggtitle(paste0("EmbedSOM: ",raw_data)) +
  theme(plot.title = element_text(size = 10, face = "bold"),panel.background = element_rect(fill='white', colour='white'))
)


ggsave("embedsom-contour.png", dpi=100,
ggplot(data_plot, aes(x = EmbedSOM1, y = EmbedSOM2, color = Cluster)) +
  geom_point(aes(colour = as.factor(labels)),
             size = .5, alpha=.3) +
  geom_density_2d(bins=6, color='black') +
  scale_color_manual(name = "Cluster",
                     values = c("1" = "#F8766D",
                                "2" = "#CD9600",
                                "3" = "#7CAE00",
                                "4" = "#00BE67",
                                "5" = "#00BFC4",
                                "6" = "#00A9FF",
                                "7" = "#C77CFF",
                                "8" = "#FF61CC")) +
  guides(colour = guide_legend(override.aes = list(size=5))) +
  coord_fixed(ratio = 1) +
  ggtitle(paste0("EmbedSOM: ",raw_data)) +
  theme(plot.title = element_text(size = 10, face = "bold"),panel.background = element_rect(fill='white', colour='white'))
)