R/coinfection_rate_histogram.R

In NCI-CGR/TypeSeq2: TypeSeq2 HPV Analysis Functions and Workflows

#'
coinfection_rate_histogram <- function(df, output_prefix=NULL){

      coinfectionRateHistrogramDf = df %>%
      filter(!is.na(Project)) %>%
      group_by(Project) %>%
      do({

      project_id = .$Project[1]

      temp = as_tibble(.) %>%
      group_by(Num_Types_Pos) %>%
      summarize(count = n())

      coinfectionRateHistogram = ggplot(temp, aes(Num_Types_Pos, count)) +
      geom_bar(stat="identity", fill="#DF8F44FF") +
      theme_light() +
      theme(
            axis.text.y = element_text(angle = 0, hjust = 1, color = "darkblue", size = 10),
            axis.text.x = element_text(hjust = 0.5),
            axis.line = element_line(colour = "darkblue",  size = 2, linetype = "solid")) +
      theme(strip.background = element_blank(),
            legend.position="none") +
      labs(title=paste0("Coinfection Rate for Project -- ", project_id), x= "Unique HPV Types Detected", y = "Number of Samples") +
      theme(
      panel.background = element_rect(fill = "white"),
      plot.margin = margin(0.5, 0.5, 0.5, 0, "cm"),
      plot.background = element_rect(
      fill = "grey90",
      colour = "black",
      size = 1)) +
      scale_x_continuous(breaks=c(0:max(df$Num_Types_Pos)), limits=c(-0.5,NA)) +
      geom_text(aes(label=count, hjust = 0.5, vjust=-0.25, size=2.75)) +
      geom_text(aes(y=count * 1.1, label="")) 

      print(coinfectionRateHistogram)

      temp = temp

      }) 

      if(!is.null(output_prefix)){
            coinfectionRateHistrogramDf %>% write_csv(sprintf("%s.coinfection_rate_histogram_plot_data.csv", output_prefix))
      }
  

      return(coinfectionRateHistrogramDf)
}