R/zzz.r

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

#' Setting up the package
#'
#' Setting theme, colors and verbosity
#' @importFrom graphics axis barplot box image lines text
#' @importFrom grDevices hcl col2rgb
#' @importFrom methods new
#' @importFrom stats dist nobs optimize pchisq variable.names optim quantile 
#' pgamma
#' @import ggplot2

zzz <- NULL  #to create a useful named help page

# SET VERSION
build <- "Jacob"

# SET VERBOSITY

# dartR functions have a verbosity parameter that sets the level of reporting
# during the execution of the function. The verbosity level, set by parameter
# 'verbose' can be one of verbose 0, silent or fatal errors; 1, begin and end;
# 2, progress log; 3, progress and results summary; 5, full report.

# SET MESSAGES COLORS

# - For fatal errors use “error” which will print the message in red. Example
# usage: stop(error(“Fatal error”)) - For warning messages use “warn” which will
# print the message in yellow. Example usage: cat(warn(“message”)) - For
# reporting messages use “report” which will print the message in green. Example
# usage: cat(report(“message”)) - For important messages use “important” which
# will print the message in blue. Example usage: cat(important(“message”)) - For
# other messages as code use “code” which will print the message in cyan.
# Example usage: cat(code(“message”))
error <- crayon::red
warn <- crayon::yellow
report <- crayon::green
important <- crayon::blue
code <- crayon::cyan

# SET GLOBAL VARIABLES FOR SIMULATION FUNCTIONS
# for gl.sim.WF.table
utils::globalVariables(c("q_neutral","chromosome_name","chunk_number","real_loc","chunk_recombination","map_resolution","gamma_scale","gamma_shape","log_mean","log_sd","rate","exp_rate","chunk_cM","loci_mutation","mutations_factor", "chunk_neutral_loci", "deleterious_factor", "h_adv", "h_del", "h_distribution_adv", "h_distribution_del", "h_intercept_adv", "h_intercept_del","h_mean_adv", "h_mean_del","h_rate_adv","h_rate_del","h_sd_adv","h_sd_del","loci_advantageous","loci_deleterious", "loci_mut_adv", "loci_mut_del","loci_mut_neu","q_adv", "q_del", "q_distribution_adv","q_distribution_del", "q_equation_adv", "q_equation_del","s_adv","s_del", "s_distribution_adv","s_distribution_del"))
# for gl.sim.WF.run
utils::globalVariables(c("chromosome_name","phase1","same_line","number_pops_phase1","population_size_phase1","gen_number_phase1","dispersal_phase1","dispersal_type_phase1","number_transfers_phase1","transfer_each_gen_phase1","variance_offspring_phase1","number_offspring_phase1","selection_phase1","Ne_phase1","Ne_fst_phase1","number_pops_phase2","population_size_phase2","gen_number_phase2","dispersal_phase2","dispersal_type_phase2","number_transfers_phase2","transfer_each_gen_phase2","variance_offspring_phase2","number_offspring_phase2","selection_phase2","Ne_phase2","Ne_fst_phase2","real_freq","real_pop_size","real_pops","recombination","recombination_males","genetic_load","natural_selection_model","mutation","mut_rate","dispersal_rate_phase1","dispersal_rate_phase2","clinal_strength", "clinal_adap","local_adap"))

# defining function "dot" from data.table package to pass CRAN checks
`.` <- list

# SET PLOTS COLORS
# Convert color names to hex RGB strings taken from function col2hex from
# package gplots 
RGB_colors <- function (cname){
  colMat <- col2rgb(cname)
  rgb(red = colMat[1, ]/255, green = colMat[2, ]/255, blue = colMat[3, 
  ]/255)
}

# function to replicate defaults colors of ggplot
discrete_palette <- function(n) {
    hues <-seq(15, 375, length = n + 1)
    return(hcl(h = hues, l = 65, c = 100)[1:n])
}

# taken from wes_palette::Zissou1
diverging_palette <-
    colorRampPalette(c("#3B9AB2", "#78B7C5", "#EBCC2A", "#E1AF00", "#F21A00"))
# creating convergent to 0 palette
cool <-
    rainbow(50, start = rgb2hsv(col2rgb("cyan"))[1], end = rgb2hsv(col2rgb("blue"))[1])
warm <-
    rainbow(50, start = rgb2hsv(col2rgb("red"))[1], end = rgb2hsv(col2rgb("yellow"))[1])
cols <- c(rev(cool), rev(warm))
convergent_palette <- colorRampPalette(cols)
# taken from adegenet
viridis_palette <-
    colorRampPalette(
        c(
            "#440154FF",
            "#482173FF",
            "#433E85FF",
            "#38598CFF",
            "#2D708EFF",
            "#25858EFF",
            "#1E9B8AFF",
            "#2BB07FFF",
            "#51C56AFF",
            "#85D54AFF",
            "#C2DF23FF",
            "#FDE725FF"
        )
    )
two_colors <- c("#3B9AB2", "#78B7C5")
two_colors_contrast <- c("deeppink", "chartreuse3")
three_colors <- c("#3B9AB2", "deeppink", "lemonchiffon")
four_colors <- c("lemonchiffon", "deeppink", "dodgerblue", "chartreuse3")
# taken from package pals palette polychrome
structure_colors <- cols <-  c( "#E4E1E3", "#F6222E", "#FE00FA", "#16FF32", 
                               "#3283FE", "#FEAF16", "#B00068", "#1CFFCE", "#90AD1C", 
                               "#2ED9FF", "#DEA0FD", "#AA0DFE", "#F8A19F", "#325A9B", 
                               "#C4451C", "#1C8356", "#85660D", "#B10DA1", "#FBE426", 
                               "#1CBE4F", "#FA0087", "#FC1CBF", "#F7E1A0", "#C075A6", 
                               "#782AB6", "#AAF400", "#BDCDFF", "#822E1C", "#B5EFB5", 
                               "#7ED7D1", "#1C7F93", "#D85FF7", "#683B79", "#66B0FF", 
                               "#3B00FB")

# SET THEME FOR PLOTS
#' dartR theme
#'
#' This is the theme used as default for dartR plots.
#' This function controls all non-data display elements in the plots.
#'
#' @param base_size base font size, given in pts.
#' @param base_family base font family
#' @param base_line_size base size for line elements
#' @param base_rect_size base size for rect elements
#' @examples
#' #ggplot(data.frame(dummy=rnorm(1000)),aes(dummy)) +
#' #geom_histogram(binwidth=0.1) + theme_dartR()
#' 

# The half-line (base-fontsize / 2) sets up the basic vertical rhythm of the
# theme. Most margins will be set to this value.  However, when we work with
# relative sizes, we may want to multiply `half_line` with the appropriate
# relative size. This applies in particular for axis tick sizes. And also, for
# axis ticks and axis titles, `half_size` is too large a distance, and we use
# `half_size/2` instead.
theme_dartR <- function(base_size = 11,
                        base_family = "",
                        base_line_size = base_size / 22,
                        base_rect_size = base_size / 22) {
    half_line <- base_size / 2
    
    # Throughout the theme, we use three font sizes, `base_size` (`rel(1)`)
    #for
    # normal, `rel(0.8)` for small, and `rel(1.2)` for large.
    
    # Elements in this first block aren't used directly, but are inherited by
    # others
    t <-
        theme(
            line = element_line(
                color = "black",
                size = base_line_size,
                linetype = 1,
                lineend = "butt"
            ),
            rect = element_rect(
                fill = "white",
                color = "black",
                size = base_rect_size,
                linetype = 1
            ),
            text = element_text(
                family = base_family,
                face = "plain",
                color = "black",
                size = base_size,
                lineheight = 0.9,
                hjust = 0.5,
                vjust = 0.5,
                angle = 0,
                margin = margin(),
                debug = FALSE
            ),
            axis.line = element_blank(),
            axis.line.x = NULL,
            axis.line.y = NULL,
            axis.text = element_text(size = rel(1), color = "black"),
            axis.text.x = element_text(margin = margin(t = 0.8 * half_line / 2),
                                       vjust = 1),
            axis.text.x.top = element_text(margin = margin(b = 0.8 * half_line / 2), vjust = 0),
            axis.text.y = element_text(margin = margin(r = 0.8 *
                                                           half_line / 2), hjust = 1),
            axis.text.y.right = element_text(margin = margin(l = 0.8 * half_line /
                                                                 2), hjust = 0),
            axis.ticks = element_line(color = "gray80"),
            axis.ticks.length = unit(half_line / 2, "pt"),
            axis.ticks.length.x = NULL,
            axis.ticks.length.x.top = NULL,
            axis.ticks.length.x.bottom = NULL,
            axis.ticks.length.y = NULL,
            axis.ticks.length.y.left = NULL,
            axis.ticks.length.y.right = NULL,
            axis.title.x = element_text(
                margin = margin(t = half_line / 2),
                vjust = 1,
                face = "bold"
            ),
            axis.title.x.top = element_text(margin = margin(b = half_line / 2), vjust = 0),
            axis.title.y = element_text(
                angle = 90,
                margin = margin(r = half_line / 2),
                vjust = 1,
                face = "bold"
            ),
            axis.title.y.right = element_text(
                angle = -90,
                margin = margin(l = half_line / 2),
                vjust = 0
            ),
            legend.background = element_rect(color = "transparent"),
            legend.spacing = unit(2 * half_line, "pt"),
            legend.spacing.x = NULL,
            legend.spacing.y = NULL,
            legend.margin = margin(half_line, half_line, half_line, half_line),
            legend.key = element_rect(fill = "white",
                                      color = NA),
            legend.key.size = unit(1.2, "lines"),
            legend.key.height = NULL,
            legend.key.width = NULL,
            legend.text = element_text(size = rel(1.2),
                                       face = "bold"),
            legend.text.align = NULL,
            legend.title = element_text(
                size = rel(1),
                face = "bold",
                hjust = 0
            ),
            legend.title.align = NULL,
            legend.position = "right",
            legend.direction = NULL,
            legend.justification = "center",
            legend.box = NULL,
            legend.box.margin = margin(0,
                                       0, 0, 0, "cm"),
            legend.box.background = element_blank(),
            legend.box.spacing = unit(2 * half_line, "pt"),
            panel.background = element_rect(fill = "white",
                                            color = NA),
            panel.border = element_blank(),
            panel.grid = element_line(color = "gray80"),
            panel.grid.minor = element_line(size = rel(0.5)),
            panel.spacing = unit(half_line, "pt"),
            panel.spacing.x = NULL,
            panel.spacing.y = NULL,
            panel.ontop = FALSE,
            strip.background = element_rect(fill = "white",
                                            color = "black"),
            strip.text = element_text(
                color = "black",
                size = rel(1),
                face = "bold",
                margin = margin(
                    0.8 * half_line,
                    0.8 *
                        half_line,
                    0.8 * half_line,
                    0.8 * half_line
                )
            ),
            strip.text.x = element_text(size = 14, face = "bold"),
            strip.text.y = element_text(angle = -90),
            strip.text.y.left = element_text(angle = 90),
            strip.placement = "inside",
            strip.placement.x = NULL,
            strip.placement.y = NULL,
            strip.switch.pad.grid = unit(half_line / 2,
                                         "pt"),
            strip.switch.pad.wrap = unit(half_line / 2, "pt"),
            plot.background = element_rect(color = "white"),
            plot.title = element_text(
                face = "bold",
                size = rel(1.2),
                hjust = 0.5,
                vjust = 1,
                margin = margin(b = half_line)
            ),
            plot.title.position = "panel",
            plot.subtitle = element_text(
                hjust = 0.5,
                vjust = 1,
                margin = margin(b = half_line)
            ),
            plot.caption = element_text(
                size = rel(0.8),
                hjust = 1,
                vjust = 1,
                margin = margin(t = half_line)
            ),
            plot.caption.position = "panel",
            plot.tag = element_text(
                size = rel(1.2),
                hjust = 0.5,
                vjust = 0.5
            ),
            plot.tag.position = "topleft",
            plot.margin = margin(half_line, half_line, half_line, half_line),
            complete = TRUE
        )
}

## plot method
# setMethod("plot", signature(x = "genlight"), function(x,
#                                                       group_pop = TRUE,
#                                                       ind_labels = TRUE,
#                                                       ind_labels_size = 8,
#                                                       plot_colors = four_colors,
#                                                       posi = "bottom",
#                                                       save2tmp = FALSE,
#                                                       verbose = NULL) {
#     gl.smearplot(
#         x,
#         group_pop = group_pop,
#         ind_labels = ind_labels,
#         ind_labels_size = ind_labels_size,
#         plot_colors = plot_colors,
#         posi = posi,
#         save2tmp = save2tmp,
#         verbose = verbose
#     )
# })

# WELCOME MESSAGE
.onAttach <- function(...) {
    packageStartupMessage(important(
        paste(
            "**** Welcome to dartR [Version",
            packageVersion("dartR"),
            "] ****\n"
        )
    ))
    packageStartupMessage(
        report(
            "Be aware that owing to CRAN requirements and compatibility reasons not all functions of the package may run after the basic installation, as some packages could still be missing. Hence for a most enjoyable experience we recommend to run the function "
        )
    )
    packageStartupMessage(code("gl.install.vanilla.dartR()"))
    
    packageStartupMessage(
        report(
            "This installs all missing and required packages for your version of dartR. In case something fails during installation please refer to this tutorial: https://github.com/green-striped-gecko/dartR/wiki/Installation-tutorial.\n\nFor information how to cite dartR, please use:"
        )
    )
    packageStartupMessage(code("citation('dartR')"))
    
    options(dartR_verbose = 2)
    packageStartupMessage(report("Global verbosity is set to: 2\n"))
    
    packageStartupMessage(important("\n**** Have fun using dartR! ****"))
}