R/ggplot_theme_pub.R

In computational-metabolomics/structtoolbox: Data processing & analysis tools for Metabolomics and other omics

#' @import ggthemes
#' @import scales
theme_Publication <- function(base_size=14){ #, base_family="helvetica") {
    (theme_foundation(base_size=base_size) #, base_family=base_family)
        + theme(plot.title = element_text(face = "bold",
            size = rel(1.2), hjust = 0.5),
            text = element_text(),
            panel.background = element_rect(colour = '#ffffff'),
            plot.background = element_rect(colour = '#ffffff'),
            panel.border = element_rect(colour = NA),
            axis.title = element_text(face = "bold",size = rel(1)),
            axis.title.y = element_text(angle=90,vjust =2),
            axis.title.x = element_text(vjust = -0.2),
            axis.text = element_text(),
            axis.line = element_line(colour="black"),
            axis.ticks = element_line(),
            panel.grid.major = element_line(colour="#f0f0f0"),
            panel.grid.minor = element_blank(),
            legend.key = element_rect(colour = '#ffffff'),
            legend.position = "bottom",
            legend.direction = "horizontal",
            legend.key.size= unit(0.75, "cm"),
            legend.spacing = unit(0.2, "cm"),
            legend.title = element_text(face="italic"),
            plot.margin=unit(c(10,5,5,5),"mm"),
            strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
            strip.text = element_text(face="bold")
        ))

}

scale_fill_Publication <- function(...){
    #library(scales)
    discrete_scale("fill","Publication",manual_pal(values = c("#386cb0","#ef3b2c","#7fc97f","#fdb462","#984ea3","#a6cee3","#778899","#fb9a99","#ffff33")), ...)
}


scale_colour_Publication <- function(...){
    #library(scales)
    discrete_scale("colour","Publication",manual_pal(values = c("#386cb0","#ef3b2c","#7fc97f","#fdb462","#984ea3","#a6cee3","#778899","#fb9a99","#ffff33")), ...)

}

createClassAndColors <- function (class, QC_label="QC", Blank_label="Blank", QC_color="#000000",
    Blank_color="#A65628",
    manual_color=c("#386cb0","#ef3b2c","#7fc97f","#fdb462","#984ea3","#a6cee3","#778899","#fb9a99","#ffff33")
)
{
    if (!is.ordered(class))
    {
        reorderNames <- sort(as.character(unique(class)))
    } else
    {
        reorderNames=levels(class)
    }

    # if too many levels then use rainbow scale with suitable number of colours
    if (length(reorderNames)>length(manual_color))
    {
        manual_color=grDevices::rainbow(length(reorderNames))
    }

    hit1 <- which(reorderNames==QC_label)
    if (length(hit1)==0) hit1 <- NULL

    hit2 <- which(reorderNames==Blank_label)
    if (length(hit2)==0) hit2 <- NULL

    if (!is.null(c(hit1,hit2)))
    {
        remo <- c(1:length(reorderNames))[-c(hit1,hit2)]
    } else
    {
        remo <- c(1:length(reorderNames))
    }

    reorderNames <- reorderNames[c(hit1, hit2,remo)]

    class <- factor (class, levels=reorderNames, ordered=TRUE)

    extraColors <- NULL
    if(!is.null(hit1)) extraColors[1] <- QC_color
    if(!is.null(hit2)) extraColors[2] <- Blank_color

    if (!is.null(extraColors)) extraColors <- extraColors[!is.na(extraColors)]

    out <- list(class=class,manual_colors=c(extraColors,manual_color))
    out
}