R/in_plotIntegration_mcca.R

In isglobal-brge/omicRexposome: Exposome and omic data associatin and integration analysis

.plot_integration_mcca <- function(object, main, tcolors, legend.show, lb.th) {

    ## Create single table will all the correlations

    all <- lapply(1:MultiDataSet::opt(object)$S, function(ii) {
        tbl <- cbind(getIntegration(object)$ws[[ii]], object@options$names[ii])
        rownames(tbl) <- rownames(object@fData[[ii]])
        colnames(tbl) <- c("x", "y", "feature")
        tbl[ tbl[ , 1] != 0 | tbl[ , 2] != 0, ]
    })
    all <- data.frame(do.call(rbind, all), stringsAsFactors = FALSE)
    all$x <- as.numeric(all$x)
    all$y <- as.numeric(all$y)
    ## /

    ## Filters for 0s
    f1 <- all[ , 1] != 0 & all[ , 2] != 0
    f2 <- all[ , 1] == 0 | all[ , 2] == 0
    f3 <- abs(all[ , 1]) > lb.th | abs(all[ , 2]) > lb.th
    ## /

    ## Draw Circle
    theta <- c(seq(-pi, pi, length = 50), seq(pi, -pi, length = 50))
    circle <- data.frame(xcircle = cos(theta), ycircle = sin(theta))
    cplot <- ggplot2::ggplot(data = circle, ggplot2::aes_string("xcircle", "ycircle")) +
        ggplot2::geom_path(ggplot2::aes_string("xcircle", "ycircle"), color="darkgray") +
        ggplot2::geom_hline(yintercept = 0, linetype = "dashed", color="darkcyan") +
        ggplot2::geom_vline(xintercept = 0, linetype = "dashed", color="darkcyan")
    ## /

    ## Draw arrows
    if(sum(f1) != 0) {
        # cplot <- cplot + ggplot2::geom_segment(data = all[f1, 1:2],
        #     ggplot2::aes_string(x = 0, y = 0, xend = "x", yend = "y"),
        #     arrow = grid::arrow(length = grid::unit(0.2, "cm")),
        #     color = tcolors[all$feature[f1]], linetype = "solid")
        cplot <- cplot + ggplot2::geom_point(data = all[f1, ],
            ggplot2::aes_string("x", "y", color = "feature"), shape = 19, size = 1)
    }
    ## /

    ## Draw points
    if(sum(f2) != 0) {
        cplot <- cplot + ggplot2::geom_point(data = all[f2, ],
            ggplot2::aes_string("x", "y", color = "feature"), shape = 19, size = 1) +
            ggplot2::scale_color_manual(values=tcolors) +
            ggplot2::theme(legend.title = ggplot2::element_blank()) +
            ggplot2::scale_y_continuous("Second Component") +
            ggplot2::scale_x_continuous("First Component")
    }
    ## /

    ## Add labels for features
    all$label <- rownames(all)
    cplot <- cplot + ggrepel::geom_text_repel(
        data = subset(all, abs(all$x) >= lb.th | abs(all$y) >= lb.th),
        ggplot2::aes_string("x", "y", label="label"),
        size = 2,
        box.padding = ggplot2::unit(0.35, "lines"),
        point.padding = ggplot2::unit(0.3, "lines"),
        color="#222222",
        segment.color="#BBBBBB"
    ) + ggplot2::theme_bw() + ggplot2::theme(legend.position="none")
    ## /

    ## Extra bar charts
    uplot <- ggplot2::ggplot(all, ggplot2::aes_string(x="x", y="x", color="feature", fill="feature")) +
        ggplot2::geom_bar(stat="identity") +
        ggplot2::scale_x_continuous(limits = c(-1, 1)) +
        ggplot2::scale_y_continuous(limits = c(-1, 1)) +
        ggplot2::scale_color_manual(values=tcolors) +
        ggplot2::scale_fill_manual(values=tcolors) +
        ggplot2::theme_bw() +
        ggplot2::theme(
            legend.position="none",
            axis.title.x=ggplot2::element_blank(),
            axis.text.x=ggplot2::element_blank(),
            axis.ticks.x=ggplot2::element_blank()
        ) + ggplot2::ylab("First Component") +
        ggplot2::geom_vline(xintercept = 0, linetype = "dashed", color="darkcyan")
    rplot <- ggplot2::ggplot(all, ggplot2::aes_string(x="y", y="y", color="feature", fill="feature")) +
        ggplot2::geom_bar(stat="identity") +
        ggplot2::scale_x_continuous(limits = c(-1, 1)) +
        ggplot2::scale_y_continuous(limits = c(-1, 1)) +
        ggplot2::scale_color_manual(values=tcolors) +
        ggplot2::scale_fill_manual(values=tcolors) +
        ggplot2::theme_bw() +
        ggplot2::theme(
            legend.title=ggplot2::element_blank(),
            axis.title.y=ggplot2::element_blank(),
            axis.text.y=ggplot2::element_blank(),
            axis.ticks.y=ggplot2::element_blank()
        ) + ggplot2::ylab("Second Component") +
        ggplot2::geom_vline(xintercept = 0, linetype = "dashed", color="darkcyan") +
        ggplot2::coord_flip()
    ##

    ## Add titles
    if(missing(main)) {
        uplot <- uplot + ggplot2::ggtitle(paste0("Crossomics\n", paste(names(object@fData), collapse = " - "))) +
            ggplot2::theme(plot.title = ggplot2::element_text(lineheight = 0.8, face = "bold"))
    } else {
        uplot <- uplot + ggplot2::ggtitle(main) +
            ggplot2::theme(plot.title = ggplot2::element_text(lineheight = 0.8, face = "bold"))
    }
    ## /

    ## Add legend
    if(legend.show == FALSE) {
        rplot <- rplot +  ggplot2::theme(legend.position="none")
    }
    ##

    ## Empty
    empty <- ggplot2::ggplot() +
        ggplot2::geom_point(ggplot2::aes(1,1), colour="white")+
        ggplot2::theme(
            axis.ticks=ggplot2::element_blank(),
            panel.background=ggplot2::element_blank(),
            axis.text.x=ggplot2::element_blank(),
            axis.text.y=ggplot2::element_blank(),
            axis.title.x=ggplot2::element_blank(),
            axis.title.y=ggplot2::element_blank()
        )
    ##
    return(gridExtra::grid.arrange(uplot, empty, cplot, rplot, ncol=2, nrow=2, widths=c(4, 1), heights=c(1, 4)))
}