R/epi_plot_heatmap.R

In AntonioJBT/episcout: Quickly Clean, Explore and Visualise Large Epidemiological Datasets

#' @title Plot a simple heatmap using ggplot2
#'
#' @description Plot correlations between numeric variables as a heatmap using
#' ggplot2. Pass the correlation values from a melted (long) correlation matrix as
#' input.
#'
#' @param cormat_melted a matrix object (usually the output of Hmisc::rcorr()
#' r (or P) or episcout::epi_stats_corr()). Default is 'cormat_all$cormat_melted_r'
#'
#' @param title Main title for the plot. Default is blank ('')
#'
#' @return Returns a heatmap as a ggplot2 object
#'
#' @author Antonio Berlanga-Taylor <\url{https://github.com/AntonioJBT/episcout}>
#'
#' @seealso \code{\link{epi_stats_corr}},
#' \code{\link{epi_stats_corr_triangle}},
#' \code{\link{epi_stats_corr_rename}},
#' \code{\link{epi_plot_heatmap_triangle}}
#'
#' @examples
#'
#' \dontrun{
#' df <- data.frame(var_id = rep(1:(n / 2), each = 2),
#' var_to_rep = rep(c("Pre", "Post"), n / 2),
#' x = rnorm(n),
#' y = rbinom(n, 1, 0.50),
#' z = rpois(n, 2)
#' )
#' df_corr <- df %>% select_if(~ epi_clean_cond_numeric(.))
#' df_corr <- df_corr[, -1] # exclude var_id
#' cormat_all <- epi_stats_corr(df_corr, method = 'pearson')
#' melted_triangles <- epi_stats_corr_triangle(cormat = cormat_all$cormat)
#' vars_list <- c('x', 'y', 'z')
#' var_labels <- c('numeric', 'binomial', 'poisson')
#' renamed_triangles <- epi_stats_corr_rename(melted_triangles$cormat_melted_triangle_r,
#'                                            melted_triangles$cormat_melted_triangle_pval,
#'                                            vars_list = vars_list,
#'                                            var_labels = var_labels
#'                                            )
#' library(ggplot2)
#' library(ggthemes)
#' epi_plot_heatmap(cormat_all$cormat_melted_r)
#' epi_plot_heatmap(renamed_triangles$cormat_melted_triangle_r)
#' epi_plot_heatmap(renamed_triangles$cormat_melted_triangle_pval)
#' ggsave('my_heatmap.svg')
#' }
#' @export
#'

epi_plot_heatmap <- function(cormat_melted = 'cormat_all$cormat_melted_r',
                             title = ''
                             ) {
  if (!requireNamespace('ggplot2', quietly = TRUE)) {
    stop('Package ggplot2 needed for this function to work. Please install it.',
         call. = FALSE)
  }
  heat_map <- ggplot2::ggplot(data = as.data.frame(cormat_melted),
                              ggplot2::aes_string(x = 'Var1',
                                                  y = 'Var2',
                                                  fill = 'value')
                              ) +
    ggplot2::geom_tile() +
    ggplot2::labs(title = title,
                  y = '',
                  x = '') +
    epi_plot_theme_2() +
    ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90,
                                                       vjust = 0.5),
                   plot.title = ggplot2::element_text(hjust = 0.5)
                   )
  return(heat_map)
}