plot_overPass.R

#!/usr/bin/env Rscript
# R-script to process and plot tag usage data world-wide
# usage: ./plot_overPass.R [-i input.csv] [-o output.png|.jpg|.pdf] [--tag1 old=tag] [--tag2 new=tag]
#        -i|--input         - input file in csv format with header [default or -: stdin]
#        -o|--output        - output picture file formats: png, jpg, pdf (default: .png with autogenerated name)
#        -t|--tag1          - name of subject tag, must match header (default: taken from second-last header value)
#        -n|--tag2          - name of tag for comparison, must match header (default: taken from last header value)
#        -c|--color         - color scheme for the plot: green-red, blue-red, viridis, plasma [GR, BR, V, P] (default: GR)
#
# pipe: ./csv_compare_tags.sh | ./plot_overPass.R 

args = commandArgs(trailingOnly = TRUE)

# Load packages
    packages = c("tidyverse", "ggspatial", "sf", "rnaturalearth", 
                 "rnaturalearthdata", "rgeos", "cowplot", "optparse", "ggtext")

    pack_check <- lapply(packages,
                           FUN = function(x) {
                                                if (!require(x, character.only = TRUE)) {
                                                  install.packages(x, dependencies = TRUE)
                                                  library(x, character.only = TRUE)
                                                }
                                              }
                        )

# Read options
    option_list <- list(
                        make_option(c("-i", "--input", type="character"),
                                        default = NULL, help = 'Input CSV file with counts',
                                        metavar = 'character'),
                        make_option(c("-o", "--output", type="character"),
                                        default = paste0("plot_", format(Sys.time(), "%y%m%d_%H%M%S"), ".png"),
                                        help = 'Outputfile for plot (.png, ,jpg, .pdf)',
                                        metavar = 'character'),
                        make_option(c("-t", "--tag1", type="character"),
                                        default = NULL, help = 'Old tag name',
                                        metavar = 'character'),
                        make_option(c("-n", "--tag2", type="character"),
                                        default = NULL, help = 'New tag name',
                                        metavar = 'character'),
                        make_option(c("-c", "--color", type="character"),
                                        default = "GR", help = 'Color scheme for plot (GR, BR, V, P)',
                                        metavar = 'character'))

    opt_parser <- OptionParser(option_list = option_list)
    opt <- parse_args(opt_parser)
    

# Get data about countries
    world <- ne_countries(scale = "medium", returnclass = "sf")

# Load overpass data
    if (opt$input == "-" || is.null(opt$input)) {
        overpass <- read_csv(file("stdin"), na = "")
    } else {
        overpass <- read_csv(opt$input, na = "")
    }

# Get names of the tags
    if (is_null(opt$tag1)) {
        tag1 <- rev(names(overpass))[2]
        tag1 <- rlang::sym(tag1)
    } else {
        tag1 <- rlang::sym(opt$tag1)
    }

    if (is_null(opt$tag2)) {
        tag2 <- rev(names(overpass))[1]
        tag2 <- rlang::sym(tag2)
    } else {
        tag2 <- rlang::sym(opt$tag2)
    }

# Calculate persent used
    overpass <- overpass %>%
                    mutate(percent = !!tag1 / (!!tag1 + !!tag2) * 100)

# Merge world with overpass data
    plot <- world %>% 
                left_join(overpass, by = c("iso_a2" = "iso_a2")) %>%
                ggplot() +
                    geom_sf(aes(fill = percent),  color = "black", size = 0.1) +
                    coord_sf(expand = FALSE, ylim = c(-55, 90)) +
                    scale_y_continuous(breaks = c(-50, 0 , 50)) +
                    theme_minimal() +
                    theme( plot.title.position = "plot",
                           plot.title = element_markdown(size = 11))
    
    if (opt$color == "V"){
        plot <- plot +
                    scale_fill_viridis_c(option = "viridis",
                                         name = "%",
                                         limits = c(0,100)) +
                    labs(title = paste0("Country preference for <span style = 'color:#DCE319FF;'>**", tag1, "**</span>
                              vs. <span style = 'color:#482677FF;'>**", tag2, "**</span>"),
                         caption = Sys.Date())
    } else if (opt$color == "P") {
        plot <- plot +
                    scale_fill_viridis_c(option = "plasma",
                                         name = "%",
                                         limits = c(0,100)) +
                    labs(title = paste0("Country preference for <span style = 'color:#F7E225FF;'>**", tag1, "**</span>
                              vs. <span style = 'color:#2D0594FF;'>**", tag2, "**</span>"),
                         caption = Sys.Date())
    } else if (opt$color == "BR") {
        plot <- plot +
                    scale_fill_gradient2(name = "%",
                                         low = "dodgerblue3",
                                         mid = "white",
                                         high = "red3",
                                         midpoint = 50,
                                         limits = c(0,100)) +
                    labs(title = paste0("Country preference for <span style = 'color:red3;'>**", tag1, "**</span>
                              vs. <span style = 'color:dodgerblue3;'>**", tag2, "**</span>"),
                         caption = Sys.Date())
    } else {
        plot <- plot +
                    scale_fill_gradient2(name = "%",
                                         low = "darkgreen",
                                         mid = "white",
                                         high = "red3",
                                         midpoint = 50,
                                         limits = c(0,100)) +
                    labs(title = paste0("Country preference for <span style = 'color:red3;'>**", tag1, "**</span>
                              vs. <span style = 'color:darkgreen;'>**", tag2, "**</span>"),
                         caption = Sys.Date())
    }
        
# Save output figure
    save_plot(opt$output, plot)