R/plothomolplotly.R

In blosloos/nontarget: Detecting Isotope, Adduct and Homologue Relations in LC-MS Data

#'description
#' paramater explanation
#'

#'@export
#'@import plotly
#'@import tibble
#'@import ggplot2
#'@import tidyverse
#'@import tidyr
###############################################################################
plothomolplotly <- function(homol) {

  homo_tibble <- tibble::as_tibble(homol[[1]])
  
  homo_tibble <- homo_tibble %>%
    plotly::mutate(hsid = homo_tibble$`HS IDs`) %>%
    plotly::mutate(mzsplit = homo_tibble$'m/z increment') %>%
    tidyr::separate_rows(c('hsid', 'mzsplit'), sep = "/") %>%
    plotly::mutate(hsid = as.factor("hsid"))
  
  summary(homo_tibble)
  homo_filter <- homo_tibble %>%
    filter(homo_tibble$"HS IDs" != "0")

  # grouping mz increments for plot legend/interactive plotly
  homo_filter$mzsplit <- as.numeric(homo_filter$mzsplit)
  homo_filter$delta_mz = NA
  homo_filter$delta_mz[homo_filter$mzsplit < 14] = "x <14"
  homo_filter$delta_mz[homo_filter$mzsplit < 15 &
                         homo_filter$mzsplit > 14] = ">14 x <15"
  homo_filter$delta_mz[homo_filter$mzsplit < 18 &
                         homo_filter$mzsplit > 15] = ">15 x <18"
  homo_filter$delta_mz[homo_filter$mzsplit < 21 &
                         homo_filter$mzsplit > 18] = ">18 x <21"
  homo_filter$delta_mz[homo_filter$mzsplit < 30 &
                         homo_filter$mzsplit > 21] = ">21 x <30"
  homo_filter$delta_mz[homo_filter$mzsplit < 32 &
                         homo_filter$mzsplit > 30] = ">30 x <32"
  homo_filter$delta_mz[homo_filter$mzsplit < 60 &
                         homo_filter$mzsplit > 32] = ">32 x <60"
  homo_filter$delta_mz[homo_filter$mzsplit < 90 &
                         homo_filter$mzsplit > 60] = ">60 x <90"
  homo_filter$delta_mz[homo_filter$mzsplit < 120 &
                         homo_filter$mzsplit > 90] = ">90 x <120"
  homo_filter$delta_mz[homo_filter$mzsplit < 150 &
                         homo_filter$mzsplit > 120] = ">120 x <150"
  homo_filter$delta_mz[homo_filter$mzsplit < 200 &
                         homo_filter$mzsplit > 150] = ">150 x <200"
  
  neworderLegend = c("x <14",
                     ">14 x <15",
                     ">15 x <18",
                     ">18 x <21",
                     ">21 x <30",
                     ">30 x <32",
                     ">32 x <60")
  homo_filter$delta_mz <-
    factor(homo_filter$delta_mz, levels = neworderLegend)
  
  homo_plot <-
    ggplot2::ggplot(data = homo_filter, aes(
      x = "RT",
      y = "mz",
      text = paste(
        "m/z increment ",
        homo_filter$`m/z increment`,
        "\n",
        "HS ID ",
        homo_filter$`HS IDs`,
        "\n",
        sep = ""
      )
    )) +
    labs(title = "homologue series") +
    geom_line(
      data = homo_filter,
      aes(
        x = "RT",
        y = "mz",
        group = "hsid",
        color = "delta_mz",
        alpha = 1
      ),
      lwd = 1
    ) + #x=mz, y=rt
    geom_point(alpha = 1,
               color = "darkgrey",
               size = 0.7) +
    theme_bw()
  
  ggplotly_homo_plot <-
    plotly::ggplotly(homo_plot) %>% plotly::add_annotations(
      text = "m/z increment",
      xref = "paper",
      yref = "paper",
      x =
        1.02,
      xanchor = "left",
      y =
        0.8,
      yanchor = "bottom",
      # Same y as legend below
      legendtitle =
        TRUE,
      showarrow = FALSE
    ) %>%
    plotly::layout(legend = list(y = 0.8, yanchor = "top"))
  
  ggplotly_homo_plot
}