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ProjectTILs/ProjectTILS_CART.R

+library(ProjecTILs)
+library(Seurat)
+library(ggplot2)
+library(patchwork)
+library(SignatuR)
+library(UCell)
+
+# Load Referece
+wdir <- "./ProjectTILs"
+ref <- load.reference.map(paste(wdir, "ref_TILAtlas_mouse_v1.rds", sep = "/"))
+
+####################
+#### CART MAGIC ####
+####################
+obj <- readRDS(paste(wdir, "Full_CART.rds", sep = "/"))
+
+# Project data by subject (two mice separately)
+query.list <- SplitObject(obj, split.by = "orig.ident")
+query.projected <- make.projection(query.list, ref = ref, ncores = 2)
+query.projected.merged <- Reduce(f = merge.Seurat.embeddings, x = query.projected)
+query.projected <- SplitObject(query.projected.merged, split.by = "PROP.Condition")
+
+plots <- list()
+lgt <- length(query.projected)
+palette <- ref@misc$atlas.palette
+for (i in seq_along(query.projected)) {
+  sample <- names(query.projected)[i]
+  plots[[i]] <- plot.projection(ref, query.projected[[i]], linesize = 0.5, pointsize = 0) +
+    ggtitle(sample) +
+    NoLegend() +
+    ylim(-10, 10)
+}
+
+png(file = paste(wdir, "Full_WPRE_CART_TILs.png", sep = "/"), width = 1400, height = 400)
+wrap_plots(plots, ncol = 4)
+dev.off()
+
+#### Barplot
+tb.full <- data.frame()
+palette <- ref@misc$atlas.palette
+for (i in seq_along(query.projected)) {
+  sample <- names(query.projected)[i]
+  print(sample)
+  query.projected[[i]] <- cellstate.predict(ref = ref, query = query.projected[[i]], reduction = "umap")
+  metric <- "percent"
+  labels.col <- "functional.cluster"
+  labels <- ref[[labels.col]][,1]
+  states_all <- levels(factor(labels))
+  query = query.projected[[i]]
+  tb <- table(factor(query[[labels.col]][,1], levels=states_all))
+  if (metric=="percent") {  #normalize
+    tb <- tb*100/sum(tb)
+    tb.m <- reshape2::melt(tb)
+    colnames(tb.m) <- c("Cell_state","Perc_cells")
+  } else if (metric=="count") {
+    tb.m <- reshape2::melt(tb)
+    colnames(tb.m) <- c("Cell_state","Ncells")
+  } else {
+    stop("Unknown metric specified (Must be either 'count' or 'percent')")
+  }
+  tb.m$Group <- sample
+  tb.full <- rbind(tb.full, tb.m)
+}
+
+tb.full$Group <- factor(tb.full$Group, levels = c("Empty", "Ortho", "IFN", "P2A"))
+p <- ggplot(data = tb.full, mapping = aes(x = Group, y = Perc_cells, fill = Cell_state)) +
+  theme_bw(base_size = 18) +
+  theme(axis.text.x = element_blank(),
+        axis.ticks.x = element_blank(),
+        strip.background = element_rect(fill = "white", color = "white")) +
+  geom_bar(stat = "identity", position = "stack", width = 1) +
+  scale_fill_manual(values = palette, name = "Treatment") +
+  scale_y_continuous(n.breaks = 10) +
+  ggtitle("Cd8+ WPRE+") +
+  ylab("% Cells") +
+  xlab("") +
+  facet_grid(.~Group, scales = "free_x")
+
+ggsave(filename = paste(wdir, "Full_WPRE_CART_TILs_barplot.png", sep = "/"), width = 7, height = 7)
+
+
+########################
+#### CART MAGIC Neg ####
+########################
+obj <- readRDS(paste(wdir, "Full_CART_Neg_final.rds", sep = "/"))
+
+# Project data by subject (two mice separately)
+query.list <- SplitObject(obj, split.by = "orig.ident")
+query.projected <- make.projection(query.list, ref = ref, ncores = 2)
+query.projected.merged <- Reduce(f = merge.Seurat.embeddings, x = query.projected)
+query.projected <- SplitObject(query.projected.merged, split.by = "PROP.Condition")
+
+plots <- list()
+lgt <- length(query.projected)
+palette <- ref@misc$atlas.palette
+for (i in seq_along(query.projected)) {
+  sample <- names(query.projected)[i]
+  plots[[i]] <- plot.projection(ref, query.projected[[i]], linesize = 0.5, pointsize = 0) +
+    ggtitle(sample) +
+    NoLegend() +
+    ylim(-10, 10)
+}
+
+png(file = paste(wdir, "Full_WPRE_CART_Neg_TILs.png", sep = "/"), width = 1400, height = 400)
+wrap_plots(plots, ncol = 4)
+dev.off()
+
+#### Barplot
+tb.full <- data.frame()
+palette <- ref@misc$atlas.palette
+for (i in seq_along(query.projected)) {
+  sample <- names(query.projected)[i]
+  print(sample)
+  query.projected[[i]] <- cellstate.predict(ref = ref, query = query.projected[[i]], reduction = "umap")
+  metric <- "percent"
+  labels.col <- "functional.cluster"
+  labels <- ref[[labels.col]][,1]
+  states_all <- levels(factor(labels))
+  query = query.projected[[i]]
+  tb <- table(factor(query[[labels.col]][,1], levels=states_all))
+  if (metric=="percent") {  #normalize
+    tb <- tb*100/sum(tb)
+    tb.m <- reshape2::melt(tb)
+    colnames(tb.m) <- c("Cell_state","Perc_cells")
+  } else if (metric=="count") {
+    tb.m <- reshape2::melt(tb)
+    colnames(tb.m) <- c("Cell_state","Ncells")
+  } else {
+    stop("Unknown metric specified (Must be either 'count' or 'percent')")
+  }
+  tb.m$Group <- sample
+  tb.full <- rbind(tb.full, tb.m)
+}
+
+tb.full$Group <- factor(tb.full$Group, levels = c("Empty", "Ortho", "IFN", "P2A"))
+p <- ggplot(data = tb.full, mapping = aes(x = Group, y = Perc_cells, fill = Cell_state)) +
+  theme_bw(base_size = 18) +
+  theme(axis.text.x = element_blank(),
+        axis.ticks.x = element_blank(),
+        strip.background = element_rect(fill = "white", color = "white")) +
+  geom_bar(stat = "identity", position = "stack", width = 1) +
+  scale_fill_manual(values = palette, name = "Treatment") +
+  scale_y_continuous(n.breaks = 10) +
+  ggtitle("Cd8+ WPRE-") +
+  ylab("% Cells") +
+  xlab("") +
+  facet_grid(.~Group, scales = "free_x")
+
+ggsave(filename = paste(wdir, "Full_WPRE_CART_Neg_TILs_barplot.png", sep = "/"), width = 7, height = 7)