plot.R

#!/usr/bin/env Rscript
library(argparse)
library(ggplot2)
library(dplyr)
library(scales)
# library(ggthemes)
library(ggrepel)

parser <-
  ArgumentParser(description = "", formatter_class = "argparse.RawTextHelpFormatter")
parser$add_argument("-i", "--infile", type = "character",
                    help = "result file generated by run.pl")
parser$add_argument("-o", "--outfile", type = "character",
                    default = "",
                    help = "result figure file")
parser$add_argument("--width", type = "double",
                    default = 8,
                    help = "result file width")
parser$add_argument("--height", type = "double",
                    default = 6,
                    help = "result file height")
parser$add_argument("--lx", type = "double",
                    default = 0.85,
                    help = "x of legend position")
parser$add_argument("--ly", type = "double",
                    default = 0.25,
                    help = "y of legend position")
parser$add_argument("--dpi", type = "integer",
                    default = 300,
                    help = "DPI")
parser$add_argument("--labcolor", type = "character",
                    default = "Tools",
                    help = "label of color")
parser$add_argument("--labshape", type = "character",
                    default = "Datasets",
                    help = "label of shape")
parser$add_argument(
                  "-d", "--datasets", metavar = "groups", type = "character",
                  default = "dataset_A.fa,dataset_B.fa", help = 'dataset'
)


args <- parser$parse_args()

if (is.null(args$infile)) {
  write("ERROR: Input file (generated by run.pl) needed!\n", file = stderr())
  quit("no", 1)
}
if (args$outfile == "") {
  args$outfile = paste(args$infile, ".png", sep="")
}

w <- args$width
h <- args$height

df <- read.csv(args$infile, sep = "\t")

# filter
datasets <- unlist(strsplit(args$datasets, ","))
df <- df[df$dataset %in% datasets,]

# sort
df$test <- factor(df$test, levels = unique(df$test), ordered = TRUE)
df$app <- factor(df$app, levels = unique(df$app), ordered = TRUE)
df$dataset <-
  factor(df$dataset, levels = unique(df$dataset), ordered = TRUE)

# rename dataset
# re <- function(x) {
#   if (is.character(x) | is.factor(x)) {
#     x <- gsub("\\.fa","",x)
#   }
#   return(x)
# }
# df <- as.data.frame(lapply(df, re))


# humanize mem unit
max_mem <- max(df$mem_mean)
unit <- "KB"
if (max_mem > 1024 * 1024) {
  df <- df %>% mutate(mem_mean2 = mem_mean / 1024 / 1024)
  unit <- "GB"
} else if (max_mem > 1024) {
  df <- df %>% mutate(mem_mean2 = mem_mean / 1024)
  unit <- "MB"
} else {
  df <- df %>% mutate(mem_mean2 = mem_mean / 1)
  unit <- "KB"
}

p <-
  ggplot(df, aes(
    x = mem_mean2, y = time_mean,
    color = app, shape = dataset, label = app
  )) +
  
  geom_point(size = 2) +
  geom_hline(aes(yintercept = time_mean, color = app), size = 0.1, alpha = 0.4) +
  geom_vline(aes(xintercept = mem_mean2, color = app), size = 0.1, alpha = 0.4) +
  geom_text_repel(size = 4, max.iter=400000) +
  # scale_color_wsj() +
  scale_color_manual(values = c("#b79d1a", "#ff7600", "#d20015", "#00824c", "#00518b")) +
  facet_wrap( ~ test) +
  ylim(0, max(df$time_mean)) +
  xlim(0, max(df$mem_mean2)) +
  
  # ggtitle(paste("FASTA/Q Manipulation Performance\n", test1, sep = "")) +
  ylab("Time (s)") +
  xlab(paste("Peak Memory (", unit, ")", sep = "")) +
  labs(color=args$labcolor, shape=args$labshape)

p <- p +
  theme_bw() +
  theme(
    panel.border = element_rect(color = "black", size = 1.2),
    panel.background = element_blank(),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    axis.ticks.y = element_line(size = 0.8),
    axis.ticks.x = element_line(size = 0.8),
    
    strip.background = element_rect(
      colour = "white", fill = "white",
      size = 0.2
    ),
    
    legend.text = element_text(size = 14),
    legend.position = c(args$lx,args$ly),
    legend.background = element_rect(fill = "transparent"),
    legend.key.size = unit(0.6, "cm"),
    legend.key = element_blank(),
    legend.text.align = 0,
    legend.box.just = "left",
    strip.text.x = element_text(angle = 0, hjust = 0),
    
    text = element_text(
      size = 14, family = "arial", face = "bold"
    ),
    plot.title = element_text(size = 15)
  )

if (grepl("tiff?$", args$outfile, perl=TRUE, ignore.case=TRUE)) {
  ggsave(p, file = args$outfile, width = w, height = h, dpi=args$dpi, compress="lzw")
} else {
  ggsave(p, file = args$outfile, width = w, height = h, dpi=args$dpi)
}
#   p <- p + scale_color_manual(values = rep("black", length(df$app)))
#
#   ggsave(
#     p, file = paste("benchmark-", gsub(" ", "-", tolower(test1)), ".grey.png", sep = ""), width = w, height = h
#   )