R/family_abundance_plot.R

In Chang-Yu-Chang/MigrationCommunity: Microbial Consumer-Resource Model

#' Plot the relative abundance at family level
#' @description Plot the relative abundance at family level in bar plot
#' @name relative_abundance_plot
#' @param x data frame for input. This data frame should have the following columns. time: time step of simulation;
#'  variable: consumer ID or resource ID; value: consumer or resource abundance; type: R or X;
#'  reatment: treatment name; replicate: replicate number; function_group: defined by consumer type.
#'  @return ...

family_abundance_plot <- function(
                                  x) {
  x %>%
    group_by(treatment, replicate, function_group) %>%
    # Sum up biomass at family level
    summarize(family_biomass = sum(value)) %>%
    mutate(
      family_biomass_sum = sum(family_biomass),
      family_biomass_proportion = family_biomass / family_biomass_sum
    ) %>%
    ggplot(aes(x = replicate, y = family_biomass_proportion, fill = function_group)) +
    geom_bar(stat = "identity", position = "fill") +
    facet_grid(. ~ treatment) +
    scale_x_continuous(expand = c(0, 0)) +
    scale_y_continuous(expand = c(0, 0)) +
    theme_bw() +
    guides(fill = guide_legend(title = "Family")) +
    labs(x = "replicate", y = "relative abundancee")
}