Figure S12

library(magrittr)

# Figure S12B ---------
path_to_dds_object <- "path_to_dds_object"
dds <- readRDS(path_to_dds_object)

# Transform data.
vsd <- DESeq2::vst(dds)

colors.use.treatment <- c("DMSO"         = "#A78A7F",
                          "Entinostat"   = "#9CA77F",
                          "RO31"         = "#7F9CA7",
                          "Thiostrepton" = "#8A7FA7")

# PCA plot.
p1 <- DESeq2::plotPCA(vsd, intgroup = c("treatment")) + 
      ggplot2::theme_bw(base_size = 16) + 
      ggplot2::coord_cartesian() + 
      ggplot2::scale_color_manual(values = stats::setNames(colors.use.treatment, levels(dds$treatment))) + 
      ggplot2::guides("color" = ggplot2::guide_legend(title = "Treatment", title.position = "top", title.hjust = 0.5, ncol = 2)) + 
      ggplot2::theme(legend.position = "bottom",
                     legend.title = ggplot2::element_text(face = "bold"),
                     axis.title.x = ggplot2::element_blank())
p1$labels$colour <- "Treatment"
p1$layers[[1]]$aes_params$size <- 8
p1$layers[[1]]$aes_params$alpha <- 0.75
  
p2 <- DESeq2::plotPCA(vsd, intgroup = c("model")) + 
      ggplot2::theme_bw(base_size = 16) + 
      ggplot2::coord_cartesian() + 
      ggplot2::scale_color_manual(values = c("ATRT04" = "#243a76", "ATRT08" = "#096837")) +
      ggplot2::guides("color" = ggplot2::guide_legend(title = "Model", title.position = "top", title.hjust = 0.5, ncol = 1)) + 
      ggplot2::theme(legend.position = "bottom",
                     legend.title = ggplot2::element_text(face = "bold"),
                     axis.title.y = ggplot2::element_blank(),
                     axis.text.y = ggplot2::element_blank(),
                     axis.ticks.y = ggplot2::element_blank())
p2$labels$colour <- "Model"
p2$layers[[1]]$aes_params$size <- 8
p2$layers[[1]]$aes_params$alpha <- 0.75

p3 <- DESeq2::plotPCA(vsd, intgroup = c("replicate")) + 
      ggplot2::theme_bw(base_size = 16) + 
      ggplot2::coord_cartesian() + 
      ggplot2::scale_color_manual(values = stats::setNames(SCpubr::do_ColorPalette("steelblue", opposite = TRUE), levels(dds$replicate))) +
      ggplot2::guides("color" = ggplot2::guide_legend(title = "Replicate", title.position = "top", title.hjust = 0.5, ncol = 1)) + 
      ggplot2::theme(legend.position = "bottom",
                     legend.title = ggplot2::element_text(face = "bold"),
                     axis.title.y = ggplot2::element_blank(),
                     axis.text.y = ggplot2::element_blank(),
                     axis.ticks.y = ggplot2::element_blank(),
                     axis.title.x = ggplot2::element_blank())
p3$labels$colour <- "Replicate"
p3$layers[[1]]$aes_params$size <- 8
p3$layers[[1]]$aes_params$alpha <- 0.5

p <- p1 | p2 | p3

# Figure S12C ---------
path.to.activities <- "path_to_activities"
list.activities <- readRDS("/omics/odcf/analysis/hipo/hipo_049/ATRT/ATRT_Publication_GitHub/datasets/ATRT_RNA_bulk_activities.rds")

path.to.metadata <- "path_to_metadata"
metadata <- readRDS(path.to.metadata)

list.heatmaps <- list()

activities <- list.activities[["SC_Markers"]]
  
colors.use.model <- c("ATRT04" = "#243a76", "ATRT08" = "#096837")
colors.use.treatment <- c("DMSO"         = "#A78A7F",
                          "Entinostat"   = "#9CA77F",
                          "RO31"         = "#7F9CA7",
                          "Thiostrepton" = "#8A7FA7")


for (model in c("AT04", "AT08")){
  
  act <- activities[stringr::str_detect(activities$condition, model), ]
  metadata.use <- metadata[stringr::str_detect(metadata$condition, model), c("treatment", "model")]
  colnames(metadata.use) <- c("Treatment", "Model")
  
  acts_wide <- act %>% 
               tidyr::pivot_wider(id_cols = "condition", names_from = "source", values_from = "score") %>% 
               tibble::column_to_rownames(var = "condition") %>% 
               as.matrix() 
  
  p <- pheatmap::pheatmap(mat = t(acts_wide),
                          scale = "row",
                          cluster_rows = FALSE,
                          cluster_cols = FALSE,
                          treeheight_row = 0,
                          treeheight_col = 0,
                          fontsize = 16,
                          annotation_col = metadata.use,
                          color = grDevices::colorRampPalette(colors = rev(RColorBrewer::brewer.pal("RdBu", n = 11)))(100),
                          annotation_colors = list("Model" = colors.use.model,
                                                   "Treatment" = colors.use.treatment),
                          border_color = "white",
                          gaps_column = c(2, 4, 6)) %>% 
     ggplotify::as.ggplot()
  list.heatmaps[[model]] <- p
}
p <- list.heatmaps$AT04 | list.heatmaps$AT08