R/get_SD_vs_Median.R

In cautree/qa:

#' create get_median_vs_SD scatter plot
#'
#' This function loads a file as a dataframe, create scatter plot for median vs SD
#' @param infile Path to the input file
#' @return a ggplot scatter plot
#' @export
#'

get_median_vs_SD = function(input_df) {

  rownames(input_df) = input_df$plate_well
  
  df_pp = subset(input_df, is.na(subjectId))
  
  df_pp = df_pp %>%
    dplyr::select(-subjectId, -year, -plate_well)
  
  df_pp <- df_pp[,colSums(is.na(df_pp))<nrow(df_pp)]
  
  
  df_sample = subset(input_df, !is.na(subjectId))
  
  df_sample = df_sample %>%
    dplyr::select(-year, -subjectId, -plate_well)
  
  df_sample <- df_sample[,colSums(is.na(df_sample))<nrow(df_sample)]
  
  
  
  common = intersect(names(df_sample), names(df_pp))
  
  df_sample = df_sample[ , colnames(df_sample) %in%  common]
  
  df_pp = df_pp[ , colnames(df_pp) %in%  common]
  
  
  
  
  sd_df=as.data.frame(sapply(df_sample, stats::sd, na.rm = TRUE))
  
  names(sd_df) = "SD"
  
  median_df=as.data.frame(sapply(df_sample, stats::median, na.rm = TRUE))
  
  names(median_df) = "median"
  
  sample_sd_median = merge(sd_df, median_df, by=0)
  
  sample_sd_median$group = "sample"
  
  
  
  sd_df_pp=as.data.frame(sapply(df_pp, stats::sd, na.rm = TRUE))
  
  names(sd_df_pp) = "SD"
  
  median_df_pp=as.data.frame(sapply(df_pp, stats::median, na.rm = TRUE))
  
  names(median_df_pp) = "median"
  
  pp_sd_median = merge(sd_df_pp, median_df_pp, by=0)
  
  pp_sd_median$group = "pp"
  
  
  
  
  
  sd_median_df_all =rbind(sample_sd_median, pp_sd_median )
  
  
  eico_sd_median_df=sd_median_df_all[ grep("Eico_mzid", sd_median_df_all$Row.names ), ]
  
  eico_sd_median_df = eico_sd_median_df %>%
    dplyr::mutate(subgroup = "eico")
  
  
  ffa_sd_median_df= sd_median_df_all[ grep("FFA_mzid", sd_median_df_all$Row.names), ]
  
  ffa_sd_median_df = ffa_sd_median_df %>%
    dplyr::mutate(subgroup = "ffa")
  
  ba_sd_median_df= sd_median_df_all[ grep("BA_mzid", sd_median_df_all$Row.names), ]
  
  ba_sd_median_df = ba_sd_median_df %>%
    dplyr::mutate(subgroup = "ba")
  
  fah_sd_median_df= sd_median_df_all[ grep("FAH_mzid", sd_median_df_all$Row.names), ]
  
  fah_sd_median_df = fah_sd_median_df %>%
    dplyr::mutate(subgroup = "fah")
  
  
  sd_median_df_with_subgroup = rbind(eico_sd_median_df,
                                     ffa_sd_median_df,
                                     ba_sd_median_df,
                                     fah_sd_median_df )
  
  
  sd_median_df_with_subgroup %>%
    ggplot2::ggplot(aes(median, SD, color= subgroup)) +
    ggplot2::geom_point(size=0.5)+
    ggplot2::ggtitle("all metabolites median vs SD") +
    ggplot2::facet_wrap(~group) +
    ggplot2::geom_abline(intercept = 0, slope = 0.2) +
    ggplot2::xlim(0, 500000) +
    ggplot2::ylim(0, 500000) +
    ggplot2::theme(aspect.ratio=1)
  
  ggplot2::ggsave("SD_vs_Median scatter plot.pdf")
  


}