R/plot_correlationly.R

In svalvaro/MQanalyser: Analyse the proteomics LC-MS/MS data from MaxQuant.

#' Plot correlation interactively
#'
#' @param dep
#' @param intensity_type
#'
#' @return
#' @export
#'
#' @examples
plot_correlationly <- function(dep, interactive = TRUE){

    cor_mat <- stats::cor(
        SummarizedExperiment::assay(dep))

    couls <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(9, "YlGn"))

    # p <- heatmaply::heatmaply(cor_mat,
    #                      colors =  couls(256),
    #                      key.title = 'Pearson Corr.',
    #                      label_names = c('row', 'column', 'correlation')
    #                      )
    if (interactive == FALSE) {

        return(
            gplots::heatmap.2(cor_mat,
                              col = couls(20),
                              trace = 'none',
                              key.title =  'Pearson corr.',
                              density.info = 'none'
                              )
        )
    }else{
        return(
            heatmaply::heatmaply(cor_mat,
                                 colors =  couls(256),
                                 key.title = 'Pearson Corr.',
                                 label_names = c('row', 'column', 'correlation')
            )
        )
    }

    return(p)
}