R/median_vs_running_order.R

In cautree/qa:

#' A median_vs_running_order function
#'
#' This function allows you to get median vs running order
#' @param input_df, input data frame.
#' @param is_sample, boolean
#' @param df_name, name for the input data
#' @return a ggplot scatter graph
#' @export

get_median_vs_running_order = function(df_input,is_sample=TRUE, df_name="Vital") {

  df_sample <- df_input[,colSums(is.na(df_input))<nrow(df_input)]

  if("order" %in% names(df_input)){

    df_sample = df_sample %>%
      tidyr::separate(plate_well, c("plate","well"), "_") %>%
      dplyr::mutate( plate_well = paste(order, well, sep="_")) %>%
      dplyr::select(-order, -plate, -well)

  }

  rownames(df_sample) =df_sample$plate_well
  df_sample$plate_well= NULL


#########note
  df_sample = as.data.frame(t(df_sample))

  row_median = as.data.frame( sapply(df_sample, median, na.rm = TRUE))

  names(row_median) ="row_median"
 median_df = row_median %>%
    dplyr::mutate(plate_well = rownames(.)) %>%
    tidyr::separate(plate_well, c("plate", "well"), convert=TRUE) %>%
    dplyr::mutate(order =(plate-1)*96+well )%>%
    dplyr::mutate(plate = as.factor(plate))

 print(str(median_df))
 
  plt <- median_df %>%
    ggplot2::ggplot(aes(order, row_median, color = plate)) + 
    ggplot2::geom_point() +
    ggplot2::xlab("runorder") +
    ggplot2::ylab("median of metabolites in each well") +
    ggplot2::ggtitle("Median by Well vs Runorder")+
    ggplot2::theme(plot.title = element_text(hjust = 0.5))

 

  if( is_sample){

  ggsave(paste(df_name, "sample_median_vs_running_order.pdf", sep=" "), plot=plt)

  }else{
    ggsave(paste(df_name, "pp_median_vs_running_order.pdf", sep=" "), plot=plt)

  }

}