Two dimensional multi dimensional scaling (MDS) plot

mds_2d_plot.R

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#
# mds_2d_plot ----
#
################################################################################
#
# author  : talegari (Srikanth KS)
# license : GNU AGPLv3 (http://choosealicense.com/licenses/agpl-3.0/)
#
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#
# Two dimensional multi dimensional scaling (MDS) plot
#
# Arguments ----
#
#   mat      : an integer or numeric matrix
#   color_by : factor of same length as number of rows of mat. NULL by default.
#
# Value ----
#
# A ggplot object
#
# Imports/Depends ----
#
# Packages `ggplot2`, `assertthat`
#

mds_2d_plot <- function(mat, color_by = NULL){

    assertthat::assert_that(is.matrix(mat) &&
                                typeof(mat) %in% c("integer", "double")
                            )

    if(!is.null(color_by)){
        assertthat::assert_that(is.factor(color_by))
        assertthat::assert_that(length(color_by) == nrow(mat))
    }

    mat_2d <- as.data.frame(cmdscale(dist(mat),  k = 2))
    colnames(mat_2d) <- c("dim_1", "dim_2")

    if(!is.null(color_by)){

        pic <- ggplot2::qplot(dim_1
                     , dim_2
                     , data  = mat_2d
                     , color = color_by
                     , xlab  = NULL
                     , ylab  = NULL) +
               ggplot2::geom_point(alpha = 0.5)

    } else{

        pic <- ggplot2::qplot(dim_1
                     , dim_2
                     , data = mat_2d
                     , xlab  = NULL
                     , ylab  = NULL) +
               ggplot2::geom_point(alpha = 0.5)

    }
    return(pic)
}