isnb

Author: almaan

isnb/isnb.R

@@ -0,0 +1,99 @@
+#!/usr/bin/Rscript
+
+#' Code used to generate Supplementary Figure 20.
+#' Provide as input: (1) a .tsv file with the expression data, rownames
+#' should be [x_coordinate]x[y_coordinate]; and (2) a list of genes to
+#' be visualized. Output directory can be specified, default is wd.
+
+
+library(argparse)
+library(ggplot2)
+library(gridExtra)
+
+TEXT_SIZE = 25
+
+gene.plot <- function(X,
+                      col.name,
+                      size = 5
+                      ) {
+
+  x <- as.numeric(sapply(rownames(X), function(x){strsplit(x,"x")[[1]][1]}))
+  y <- as.numeric(sapply(rownames(X), function(x){strsplit(x,"x")[[1]][2]}))
+  v <- X[,col.name]
+  plotter <- data.frame(x = y, y = -x, v = v)
+  g <- ggplot(plotter,aes(x,y)) +
+    theme(text = element_text(size = TEXT_SIZE),
+          panel.background = element_rect(fill ="white",color ="white"),
+          axis.title.x = element_blank(),
+          axis.title.y = element_blank(),
+          panel.grid.major = element_blank(),
+          panel.grid.minor = element_blank(),
+          axis.line = element_blank(),
+          axis.ticks.x = element_blank(),
+          axis.ticks.y = element_blank(),
+          axis.text.x = element_blank(),
+          axis.text.y = element_blank()
+
+          ) +
+
+    labs(title = col.name) +
+    geom_point(aes(fill = v),color = "gray",size = size,shape = 21) +
+    scale_fill_gradient(low="white", high="blue",guide = F)+
+    coord_fixed()
+
+  return(g)
+}
+
+
+parser <- ArgumentParser()
+parser$add_argument("-c",
+                    "--count_data",
+                    type = "character")
+parser$add_argument("-g",
+                    "--genes",
+                    type = "character")
+parser$add_argument("-o",
+                    "--out_dir",
+                    default = NULL,
+                    type = "character")
+
+args <- parser$parse_args()
+
+if is.null(args$out_dir) {
+  args$out_dir <- getwd()
+}
+
+data <- read.table(args$count_data,
+                   sep = '\t',
+                   header = T,
+                   row.names = 1)
+
+gene.names <- as.character(unlist(read.delim(args$genes,
+                                             header = F,
+                                             sep = "\n")))
+
+elist <- list()
+for (gene in gene.names) {
+  print(gene)
+  elist[[gene]] <- gene.plot(data,
+                             gene,
+                             size = 1.8)
+}
+
+n.cols <- 3
+n.rows <- ceiling(length(genes) / n.cols)
+
+
+width <- 400*n.cols
+height <- 400*n.rows
+
+png(file.path(args$out_dir,
+              "expression-visualization.png"),
+    width = width,
+    height = height,
+    units = "px")
+
+E <- grid.arrange(grobs = elist,
+                  ncol = n.cols)
+print(E)
+dev.off()