R/plot_length_histograms.R

In NOAA-EDAB/neusCatch: Multispecies length expansion of commercial catch

#' plots length distributions
#'
#' Creates a facet plot for each market category across all years for each gear type
#'
#'@param lengthData data frame.
#'@param outputDir Character string. Path to output directory (png files saved here)
#'@param outputPlots Boolean. Should plots be created. T or F

#'
#'@importFrom ggplot2 "ggplot" "aes" "geom_bar" "geom_histogram" "facet_wrap" "element_text" "ylab" "xlab" "labs" "scale_x_discrete"
#'@importFrom dplyr "summarize" "summarise" "group_by"
#'@importFrom magrittr "%>%"
#'
#' @noRd

plot_length_histogram <- function(lengthData,outputDir,outputPlots){

  if (outputPlots == F) return()

  lengthDataGEARS <- lengthData %>%
    dplyr::group_by(NEGEAR,MARKET_CODE,LENGTH) %>%
    dplyr::summarise(numlens=sum(as.numeric(NUMLEN)))

  # check to see if any length data
  if (any(!is.na(lengthDataGEARS$LENGTH))) {


    png(paste0(outputDir,"/5a_lengths_by_gear.png"))

    p <- ggplot2::ggplot(data = lengthDataGEARS) +
      ggplot2::geom_bar(stat="identity",mapping = ggplot2::aes(x=LENGTH,y=numlens),na.rm=T) +
      ggplot2::facet_wrap(~NEGEAR,scales="free_y",nrow=length(unique(lengthData$NEGEAR)), ncol = 1) +
      # scale_x_discrete(name="Length (cm)",
      #                  breaks=seq(0,max(lengthData$LENGTH),10)) +
      ggplot2::ylab("Number at length") +
      ggplot2::xlab("Length (cm)") +
      ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, hjust = 1))
    print(p)
    dev.off()


    png(paste0(outputDir,"/5b_market_category_lengths_by_gear.png"))
    p <- ggplot2::ggplot(data = lengthDataGEARS) +
      ggplot2::geom_bar(stat="identity",mapping = ggplot2::aes(x=LENGTH,y=numlens),na.rm=T) +
      ggplot2::facet_grid(NEGEAR~MARKET_CODE,
                          scales="free_y") +
      ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, hjust = 1)) +
      #scale_x_discrete(name="Length (cm)", breaks=seq(0, max(lengthData$LENGTH),10))+
      ggplot2::xlab("Length (cm)") +
      ggplot2::ylab("Number at length")
    print(p)

    # p <- ggplot(data = lengthDataGEARS) +
    #   geom_bar(stat="identity",mapping = aes(x=LENGTH,y=numlens),na.rm=T) +
    #   facet_wrap(~NEGEAR+MARKET_CODE,scales="free_y",nrow=length(unique(lengthData$NEGEAR)), ncol = length(unique(lengthData$MARKET_CODE))) +
    #   theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
    #   scale_x_discrete(name="Length (cm)", breaks=seq(0, max(lengthData$LENGTH),10))
    # print(p)
    dev.off()




    png(paste0(outputDir,"/6_market_category_lengths.png"))
    p <- ggplot2::ggplot(data = lengthDataGEARS) +
      ggplot2::geom_bar(stat="identity",mapping = ggplot2::aes(x=LENGTH,y=numlens),na.rm=T) +
      ggplot2::facet_wrap(~MARKET_CODE,scales="free_y",nrow = length(unique(lengthData$MARKET_CODE)),ncol=1) +
      ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 90, hjust = 1)) +
      #scale_x_discrete(name="Length (cm)", breaks=seq(0, max(lengthData$LENGTH),10)) +
      ggplot2::xlab("Length (cm)") +
      ggplot2::ylab("Number at length")
    print(p)

    dev.off()
  } else {
    # no length samples
  }
}