annotate scater-plot-dist-scatter.R @ 3:8f333f90d8d6 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 9961b5acbf9081f10e14bc272406b36854fa2924"

#!/usr/bin/env Rscript

# Plot the distribution of read counts and feature counts, side by side, then a scatter plot of read counts vs feature counts below

# Load optparse we need to check inputs

library(optparse)
library(workflowscriptscommon)
library(LoomExperiment)
library(scater)
library(ggpubr)
library(scales)

# parse options

option_list <- list(
  make_option(
    c("-i", "--input-loom"),
    action = "store",
    default = NA,
    type = "character",
    help = "A SingleCellExperiment object file in Loom format."
  ),
  make_option(
    c("-o", "--output-plot-file"),
    action = "store",
    default = NA,
    type = "character",
    help = "Path of the PDF output file to save plot to."
  ),
  make_option(
    c("-l", "--log-scale"),
    action = "store_true",
    default = FALSE,
    type = "logical",
    help = "Plot on log scale (recommended for large datasets)."
  )
)

opt <- wsc_parse_args(option_list, mandatory = c("input_loom", "output_plot_file"))

# Check parameter values

if (! file.exists(opt$input_loom)) {
  stop((paste("File", opt$input_loom, "does not exist")))
}

# Filter out unexpressed features

sce <- import(opt$input_loom, format = "loom", type = "SingleCellLoomExperiment")

# Do the scatter plot of reads vs genes
total_counts <- sce$total
total_features <- sce$detected
count_feats <- cbind(total_counts, total_features)
cf_dm <- as.data.frame(count_feats)

# Calculate binwidths for reads and features plots. Use 20 bins
read_bins <- max(total_counts / 1e6) / 20
feat_bins <- max(total_features) / 20

plot1 <- qplot(total_counts / 1e6, geom = "histogram", binwidth = read_bins, ylab = "Number of cells", xlab = "Read counts (millions)", fill = I("darkseagreen3")) + ggtitle("Read counts per cell")
plot2 <- qplot(total_features, geom = "histogram", binwidth = feat_bins, ylab = "Number of cells", xlab = "Feature counts", fill = I("darkseagreen3")) + ggtitle("Feature counts per cell")
plot3 <- ggplot(cf_dm, aes(x = total_counts / 1e6, y = total_features)) + geom_point(shape = 1) + geom_smooth() + xlab("Read count (millions)") +
  ylab("Feature count") + ggtitle("Scatterplot of reads vs features")
plot4 <- plotColData(sce, y = "subsets_Mito_percent", x = "detected") + ggtitle("% MT genes") + geom_point(shape = 1) + theme(text = element_text(size = 15)) + theme(plot.title = element_text(size = 15)) + xlab("Total features") + ylab("% MT")

if (! opt$log_scale) {
  final_plot <- ggarrange(plot1, plot2, plot3, plot4, ncol = 2, nrow = 2)
  ggsave(opt$output_plot_file, final_plot, device = "pdf")
} else {
  plot1_log <- plot1 + scale_x_continuous(trans = "log10") + scale_y_continuous(trans = "log10")
  plot2_log <- plot2 + scale_y_continuous(trans = "log10")
  plot3_log <- plot3 + scale_y_continuous(trans = "log10")
  plot4_log <- plot4 + scale_y_log10(labels = number)
  final_plot_log <- ggarrange(plot1_log, plot2_log, plot3_log, plot4_log, ncol = 2, nrow = 2)
  ggsave(opt$output_plot_file, final_plot_log, device = "pdf")
}