In raphidoc/lighthouse: Database management and processing workflow for ocean optics science

require(dplyr)
require(tidyr)
require(plotly)
require(DT)
require(crosstalk)

knitr::opts_chunk$set(echo = F, cache = F, message = F, warning = F)

GLOB <- GLOB %>% mutate(QC_sign= ifelse(QC>0, "o", "x"),
                    QC_color= ifelse(QC>0, "cyan4", "red"))

GLOB_sd <- SharedData$new(GLOB, key = ~SID, group = "SPM_QC")
SPM_datatable_sd <- SharedData$new(SPM_datatable, key = ~SID, group = "SPM_QC")
Station_stats_sd <- SharedData$new(Station_stats, key = ~SID, group = "SPM_QC")
CTD_sd <- SharedData$new(CTD %>% group_by(ID), key = ~SID, group = "SPM_QC")

qc_check <- function(QC){
    if(QC < 1){
         "x"
    }
    if(QC >= 1){
         "circle"
    }
}

Column {data-width=300}

SPMs table

datatable(SPM_datatable_sd,
  extensions = c("Buttons", "Scroller", "Select"),
  filter = "top",
  escape = TRUE, rownames = FALSE,
  style = "bootstrap",
  class = "compact",
  height = 100,
  options = list(
    dom = "Brtip",
    select = list(style = 'os', items = 'row'),
    buttons = list(I("colvis"),"selectNone","csv"),
    deferRender = TRUE,
    scrollY = 100,
    pageLength = 30,
    scroller = TRUE
  ),
  selection = "none"
)

Sample statistic

datatable(Station_stats_sd,
  extensions = c("Buttons", "Scroller", "Select"),
  filter = "top",
  escape = TRUE, rownames = FALSE,
  style = "bootstrap",
  class = "compact",
  height = 100,
  options = list(
    dom = "Brtip",
    select = list(style = 'os', items = 'row'),
    buttons = list(I("colvis"),"selectNone","csv"),
    deferRender = TRUE,
    scrollY = 100,
    pageLength = 30,
    scroller = TRUE
  ),
  selection = "none"
)

Column {data-width=390}

CTD profile

Noax <- list(
  title = "Depth",
  zeroline = F,
  showline = F,
  showticklabels = T,
  showgrid = F,
  autorange = "reversed"
)

Temp <- CTD_sd %>% plot_ly(x=~Temp, y=~Depth, showlegend=T, connectgaps = F) %>% add_paths() %>%
    layout(yaxis = Noax, xaxis = list(title = "\u00B0C"))

PSU <- CTD_sd %>% plot_ly(x=~PSU, y=~Depth, showlegend=T, connectgaps = F) %>% add_paths() %>%
    layout(yaxis = Noax, xaxis = list(title = "PSU")) 

# filter_select(id = "SID",
#           label = "SID",
#           sharedData = CTD_sd,
#           group = ~SID
#           )

subplot(Temp, PSU, shareY= T, titleY = T, titleX = T) %>%
    highlight(on = "plotly_click", off = "plotly_doubleclick", selectize = F, dynamic = F, persistent = F)

Column {.tabset}

SPM vs Anap

ax <- list(
  zeroline = F,
  showline = T,
  showticklabels = T,
  showgrid = T,
  type = "log"
)

Anap_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Anap_440,
                    text=~paste0('<b>Station</b>: ', Station, '<br>',
                        '<b>ID</b>: ', ID, '\n',
                     '<b>SID</b>: ', SID, '\n',
                        '<b>Replicate</b>: ', Replicate, '\n',
                        '<b>Comment</b>: ', Comment, '\n',
                        '<b>SPM</b>: ', SPM, '\n')) %>%
    add_markers(symbol = ~as.character(QC), symbols = c("0" = "x", "1" = "o", "2" = "circle-x-open"),
              color = ~as.character(QC), colors = c("0" = "red", "1" = "cyan4", "2" = "orange")) %>%
    highlight(on = "plotly_click", off = "plotly_relayout", selectize = F, dynamic = F, persistent = F) %>%
    layout(xaxis = ax, yaxis = ax)

Anap_SPM_plot

SPM vs Aph

Aph_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Aph_532,
                    text=~paste0('<b>Station</b>: ', Station, '<br>',
                        '<b>ID</b>: ', ID, '\n',
                     '<b>SID</b>: ', SID, '\n',
                        '<b>Replicate</b>: ', Replicate, '\n',
                        '<b>Comment</b>: ', Comment, '\n',
                        '<b>SPM</b>: ', SPM, '\n')) %>%
    add_markers(symbol = ~as.character(QC), symbols = c("0" = "x", "1" = "o", "2" = "circle-x-open"),
              color = ~as.character(QC), colors = c("0" = "red", "1" = "cyan4", "2" = "orange")) %>%
    highlight(on = "plotly_click", off = "plotly_relayout", selectize = F, dynamic = F, persistent = F) %>%
    layout(xaxis = ax, yaxis = ax)

Aph_SPM_plot

SPM vs Ap

Ap_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Ap_532,
                    text=~paste0('<b>Station</b>: ', Station, '<br>',
                        '<b>ID</b>: ', ID, '\n',
                     '<b>SID</b>: ', SID, '\n',
                        '<b>Replicate</b>: ', Replicate, '\n',
                        '<b>Comment</b>: ', Comment, '\n',
                        '<b>SPM</b>: ', SPM, '\n')) %>%
    add_markers(symbol = ~as.character(QC), symbols = c("0" = "x", "1" = "o", "2" = "circle-x-open"),
              color = ~as.character(QC), colors = c("0" = "red", "1" = "cyan4", "2" = "orange")) %>%
    highlight(on = "plotly_click", off = "plotly_relayout", selectize = F, dynamic = F, persistent = F) %>%
    layout(xaxis = ax, yaxis = ax)

Ap_SPM_plot

SPM vs Bbp

Bbp_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Bbp_532,
                    text=~paste0('<b>Station</b>: ', Station, '<br>',
                        '<b>ID</b>: ', ID, '\n',
                     '<b>SID</b>: ', SID, '\n',
                        '<b>Replicate</b>: ', Replicate, '\n',
                        '<b>Comment</b>: ', Comment, '\n',
                        '<b>SPM</b>: ', SPM, '\n')) %>%
    add_markers(symbol = ~as.character(QC), symbols = c("0" = "x", "1" = "o", "2" = "circle-x-open"),
              color = ~as.character(QC), colors = c("0" = "red", "1" = "cyan4", "2" = "orange")) %>%
    highlight(on = "plotly_click", off = "plotly_relayout", selectize = F, dynamic = F, persistent = F) %>%
    layout(xaxis = ax, yaxis = ax)

Bbp_SPM_plot