summary.plots.R

summary.plots <- function(meta_data, file_name = "summary", environment = FALSE, width = 12, height =8, ... ) {
  #first Graph
  data.summary <- function(x) { #function to calculate median + sd for violin plots
  mu <- mean(x)
  sigma1 <- mu-sd(x)
  sigma2 <- mu+sd(x)
  return(c(y=mu, ymin=sigma1, ymax=sigma2))
}
  ### 1. ###################### Boxplots(gender, age) ~ status
  firstGraph <- ggplot(organ_metadata, aes(x = gender, y = age/365)) +
    geom_boxplot(data = organ_metadata, aes(color = status)) +
    xlab("Status") +
    ylab("Age") +
    scale_color_manual(values = c ("deepskyblue2", "brown3"))

  ### 2. ############## Barplot(gender) ~ group status
  secondGraph <- ggplot(organ_metadata, aes(x = gender)) + #plot age vs expression
    geom_bar(data = organ_metadata, aes(fill = status), position = position_dodge()) +
    scale_fill_manual(values = c("deepskyblue2", "brown3"))  #group and diagnsosis as factors

  ### 3. ################# Violingplots(Diagnosis, Age) with Mean and SD
  if (nlevels(organ_metadata$diagnosis) > 8) {
    coloursDiagnosis <- "Paired"
  }
  else {
    coloursDiagnosis <- "Dark2"
  }
  thirdGraph <- ggplot(organ_metadata, aes(x = diagnosis, y = age/365, color = diagnosis)) + #plot age vs expression
    geom_violin() +
    geom_jitter(size = 0.4,  width = 0.15) +
    stat_summary(fun.data = data.summary, color = "black") +
    xlab("Diagnosis") +
    ylab("Age") +
    labs(color = "Diagnosis") +
    scale_color_brewer(palette = coloursDiagnosis)

  ## 4. ################# Barplots
  xrange <- 1:nlevels(organ_metadata$diagnosis)
  fourthGraph <- ggplot(organ_metadata, aes(x = as.numeric(diagnosis) - 0.15)) + #move 0.15 to left
    geom_bar(position = "identity", width = 0.3) +
    scale_x_continuous(breaks = c(xrange), labels = unique(organ_metadata$diagnosis)) +
    labs(x = "diagnosis")+
    geom_bar(aes(x = as.numeric(diagnosis) + 0.15, fill = status), #move 0.15 to right
             position = position_dodge(), width = 0.3) +
    scale_fill_manual(values = c("deepskyblue2", "brown3")) +
    theme(axis.text = element_text(size = 7.5)) +
    facet_wrap(~gender)

  if(environment == TRUE) {
    wholeGraph <- list(firstGraph, secondGraph, thirdGraph, fourthGraph)
    return(wholeGraph)
  }

  pdf(paste0(file_name, ".pdf"), width = width, height = height)
  grid.arrange(firstGraph, secondGraph, thirdGraph, fourthGraph)
  dev.off()
}