R/plot_score_by_batch_vars_density.R

In momeara/MPStats: Tools for analyzing Morphological Profiling data

#' plot cell count by batch variables as a density plot
#' 
#'@param well_scores tibble::tibble as output by read_well_scores
#'@param subtitle plot subtitle, typically the study identifier
#'@return ggplot2 object with the lattice plot with a panel for each batch variable
#' 
#'@export 
plot_score_by_batch_vars_density <- function(well_scores, subtitle=NULL){
  data <- well_scores %>%
    dplyr::filter(!is_control) %>%
    dplyr::select(
      week, plate, row,                  # batch variables
      prob_positive)%>%                  # response values
    tidyr::pivot_longer(
      cols=c("week", "plate", "row"),
      names_to="batch_variable",
      values_to="batch_value")
  
  p <- ggplot2::ggplot(data=data) +
    ggplot2::theme_bw() +
    ggplot2::geom_density(
      mapping=ggplot2::aes(
        x=prob_positive,
        y=log10(..density..+1),
        color=batch_value,
        group=batch_value)) +
    ggplot2::facet_wrap(
      facets=ggplot2::vars(batch_variable),
      scales="free_x") +
    ggplot2::facet_wrap(
      facets=ggplot2::vars(batch_variable)) +
    ggplot2::scale_x_continuous(
      "Score",
      limits=c(0,1),
      labels=scales::percent_format()) +
    ggplot2::scale_y_continuous("log(Density+1)") +
    ggplot2::scale_color_continuous("Batch Value") +
    ggplot2::ggtitle(
      label="Classifier Score by Batch Dimensions",
      subtitle=subtitle) + 
    ggplot2::theme(
      legend.position=c(.84,1.13),
      legend.direction="horizontal",
      legend.margin=ggplot2::margin(t=0,r=0,b=0,l=0),
      legend.box.background=ggplot2::element_blank())
}