R/plot_group.R

In biocore/bayestime: (***)

#' A function to generate plots of a group of variables
#' Suggestion: take out missing values beforehand
#'
#' @param data: A dataframe with the response column to plot
#' @param time_name: the column name corresponding to the time variable in the data (string)
#' @param response_name: the column name of the intersted response variable (string)
#' @param unique_subject_id the column name corresponding to unique subject id in the data (string)
#' @param variable_name One column name of interested variable from dataset
#' @return A list with the plot and the data used for plot
#' @import ggplot2
#' @export
plot_group <- function(data, time_name, response_name,
                       unique_subject_id, variable_name){
  group <- data[, c(time_name, response_name,
                    unique_subject_id, variable_name)]
  group[, variable_name] <- as.factor(group[, variable_name])
  #group <- group[which(group[,variable_name] != 'Missing: Not provided'), ]
  time <- as.numeric(as.character(group[, time_name]))
  response <- group[, response_name]
  unique_id <- group[, unique_subject_id]
  p <- ggplot(group, aes(x = time, y = response, group = unique_id,
                         color = group[, variable_name])) +
    labs(color = variable_name) +
    geom_line(alpha = 0.2) +
    geom_smooth(se = F, size = 2, aes(group = group[, variable_name]),
                level=0.95) +
    xlab(time_name) +
    ylab(response_name) +
    theme_classic() +
    theme(plot.title = element_text(hjust = 0.5, size = 15,
                                    face = "bold"),
          axis.text.x = element_text(size = 10, face = "bold"),
          axis.text.y = element_text(size = 10, face = "bold"),
          axis.title.x = element_text(size = 12, face = "bold"),
          axis.title.y = element_text(size = 12, face = "bold"),
          legend.position = "top")

  #print(p)
  return(results <- list('data' = group,
                         'figure' = p))
}