R/plotIndiv.pls.R

In ajabadi/mixOmics2: Omics Data Integration Project

#############################################################################################################
# Authors:
#   Ignacio Gonzalez, Genopole Toulouse Midi-Pyrenees, France
#   Florian Rohart, The University of Queensland, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD
#   Benoit Gautier, The University of Queensland, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD
#   Francois Bartolo, Institut National des Sciences Appliquees et Institut de Mathematiques, Universite de Toulouse et CNRS (UMR 5219), France
#   Kim-Anh Le Cao, The University of Queensland, The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD
#
# created: 16-03-2016
# last modified: 24-08-2016
#
# Copyright (C) 2016
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
#############################################################################################################


#----------------------------------------------------------------------------------------------------------#
#-- Includes plotIndiv for PLS, sPLS, PLS-DA, SPLS-DA,  --#
#----------------------------------------------------------------------------------------------------------#
#' @title PLS sample plot methods

#' @export plotIndiv.mixo_pls

#' @export plotIndiv.mixo_spls

#' @export plotIndiv.rcc
plotIndiv.mixo_pls <-
  plotIndiv.mixo_spls <-
  plotIndiv.rcc <-  function(object,
            comp  = NULL,
            rep.space  = NULL,
            ind.names  = TRUE,
            group, # factor indicating the group membership for each sample, useful for ellipse plots. Coded as default for the -da methods, but needs to be input for the unsupervised methods (PCA, IPCA...)
            col.per.group,
            style = "ggplot2", # can choose between graphics, 3d, lattice or ggplot2
            ellipse  = FALSE, #ellipse
            ellipse.level  = 0.95,
            centroid = FALSE,  # centroid
            star = FALSE, # star
            title = NULL, #title
            subtitle,
            legend = FALSE,
            X.label  = NULL,
            Y.label  = NULL,
            Z.label  = NULL,
            abline  = FALSE, #abline
            xlim  = NULL,
            ylim  = NULL,
            col,
            cex,
            pch,
            pch.levels,
            alpha = 0.2, # used in shade3d
            axes.box  = "box",
            layout = NULL,
            size.title = rel(2),
            size.subtitle = rel(1.5),
            size.xlabel = rel(1),
            size.ylabel = rel(1),
            size.axis = rel(0.8),
            size.legend = rel(1), #size.legend
            size.legend.title = rel(1.1), #size.legend.title
            legend.title = "Legend",
            legend.title.pch = "Legend",
            legend.position = "right",
            point.lwd = 1,
            background = NULL,
            ...
)
{
    plot_parameters = list(size.title = size.title, size.subtitle = size.subtitle, size.xlabel = size.xlabel, size.ylabel = size.ylabel,
    size.axis = size.axis, size.legend = size.legend, size.legend.title = size.legend.title, legend.title = legend.title,
    legend.title.pch = legend.title.pch, legend.position = legend.position, point.lwd = point.lwd)

    if (is(object, c("mint.block.pls", "mint.block.spls", "mint.block.plsda", "mint.block.splsda")))
    stop("No plotIndiv for the following functions at this stage: mint.block.pls, mint.block.spls, mint.block.plsda, mint.block.splsda.")

    #-- choose rep.space
    if (is.null(rep.space) && is(object, "DA"))#"splsda", "plsda", "mlsplsda")))
    {
        rep.space = "X-variate"
    } else if (is.null(rep.space)) {
        rep.space = "multi"
    }
    rep.space  = match.arg(rep.space, c("XY-variate", "X-variate", "Y-variate", "multi"))
    #c("XY-variate", "X-variate", "Y-variate", "multi")[pmatch(rep.space, c("XY-variate", "X-variate", "Y-variate", "multi"))]

    if (rep.space  == "multi")
    {
        blocks = c("X", "Y")
        object$variates  = object$variates[names(object$variates) %in% blocks]
    }

    if (rep.space  == "X-variate")
    {
        object$variates  = object$variates["X"]
        blocks  = "X"
    }

    if (rep.space  == "Y-variate")
    {
        object$variates  = object$variates["Y"]
        blocks  = "Y"
    }

    if (rep.space  == "XY-variate")
    {
        object$variates$XYvariates  = (object$variates$X + object$variates$Y)/2
        object$variates  = object$variates["XYvariates"]
        blocks  = "XY combined"
    }

    if (length(blocks)!= length(unique(blocks)))
    stop("Duplicate in 'blocks' not allowed")

    if (!missing(subtitle))
    {
        if (length(subtitle)!= length(blocks) | length(subtitle)!= length(unique(subtitle)))
        stop("'subtitle' indicates the subtitle of the plot for each 'blocks'; it needs to be the same length as 'blocks' and duplicate are not allowed.")
    }

    if(!is.null(background) &&  !is(background, "background.predict"))
    stop("'background' must have been obtained with the 'background.predict' function")

    #-- check inputs
    check  = .plotIndivCheckInput(object = object, comp  = comp , blocks  = blocks, ind.names  = ind.names,
    style = style, ellipse  = ellipse, ellipse.level  = ellipse.level, centroid = centroid,
    star = star, legend = legend, X.label  = X.label, Y.label  = Y.label, Z.label  = Z.label, abline  = abline,
    xlim  = xlim, ylim  = ylim, alpha = alpha, axes.box  = axes.box, plot_parameters = plot_parameters)
    #-- retrieve outputs from the checks
    axes.box = check$axes.box
    comp = check$comp
    xlim = check$xlim
    ylim = check$ylim
    ind.names = check$ind.names
    display.names = check$display.names

    #-- get the variates
    variate = .getVariatesAndLabels(object, comp, blocks = blocks, rep.space = rep.space, style = style, X.label = X.label,
        Y.label = Y.label, Z.label = Z.label)
    #-- retrieve outputs
    x = variate$x
    y = variate$y
    z = variate$z
    X.label = variate$X.label
    Y.label = variate$Y.label
    Z.label = variate$Z.label

    n = nrow(object$X)

    # create data frame df that contains (almost) all the ploting information
    out = .inputShapePlotIndiv(object = object, n = n, blocks  = blocks, x = x, y = y, z = z, ind.names  = ind.names, group = group,
    col.per.group = col.per.group, style = style, study = "global", ellipse  = ellipse, ellipse.level  = ellipse.level,
    centroid = centroid, star = star, title = title, xlim  = xlim, ylim  = ylim,
    col = col, cex = cex, pch = pch, pch.levels = pch.levels, display.names = display.names, plot_parameters = plot_parameters)
    #-- retrieve outputs
    df = out$df
    df.ellipse = out$df.ellipse
    col.per.group = out$col.per.group
    title = out$title
    display.names = out$display.names
    xlim = out$xlim
    ylim = out$ylim
    #missing.col = out$missing.col
    ellipse = out$ellipse
    centroid = out$centroid
    star = out$star
    plot_parameters = out$plot_parameters

    # change the levels of df$Block to "subtitle"
    if (!missing(subtitle) & nlevels(df$Block)>1)#& !is.null(title)) # commented so that subtitle can be change without changing the title
    {
        df$Block = factor(df$Block, labels = subtitle)
        if (ellipse)
        df.ellipse$Block = factor(df.ellipse$Block, labels = subtitle)
    }

    # match background color to col.per.group, the color of the groups
    if(!is.null(background))
    {
        ind.match = match(names(background), levels(df$group))
        names(background) = adjustcolor(col.per.group[ind.match],alpha.f=0.1)
    }

    #save(list = ls(), file = "temp.Rdata")

    #call plot module (ggplot2, lattice, graphics, 3d)
    res = .graphicModule(df = df, centroid = centroid, col.per.group = col.per.group, title = title,
    X.label = X.label, Y.label = Y.label, Z.label = Z.label, xlim = xlim, ylim = ylim, class.object = class(object),
    display.names = display.names, legend = legend, abline = abline, star = star,
    ellipse = ellipse, df.ellipse = df.ellipse, style = style, layout = layout, #missing.col = missing.col,
    axes.box = axes.box, plot_parameters = plot_parameters, alpha = alpha, background = background)


    return(invisible(list(df = df, df.ellipse = df.ellipse, graph = res)))

}