---
title: 'SPM quality check'
output:
 flexdashboard::flex_dashboard:
   theme: "spacelab"
   source_code: embed
   orientation: columns
   vertical_layout: fill
---

```{r setup, include=FALSE, echo=TRUE, message=FALSE}
require(dplyr)
require(tidyr)
require(plotly)
require(DT)
require(crosstalk)

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

```{r sharedata objects}
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")
```

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

Column {data-width=300}
-------------------------------------

### SPMs table

```{r datatable}
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

```{r}
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 

```{r CTD ,echo=FALSE, message=FALSE}

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 

```{r SPM vs Anap ,echo=FALSE, message=FALSE}
ax <- list(
  zeroline = F,
  showline = T,
  showticklabels = T,
  showgrid = T,
  type = "log"
)

Anap_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Anap_532,
				    text=~paste0('Station: ', Station, '
',
				    	'ID: ', ID, '\n',
				     'SID: ', SID, '\n',
				    	'Replicate: ', Replicate, '\n',
				    	'Comment: ', Comment, '\n',
				    	'SPM: ', 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

```{r}
Aph_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Aph_532,
				    text=~paste0('Station: ', Station, '
',
				    	'ID: ', ID, '\n',
				     'SID: ', SID, '\n',
				    	'Replicate: ', Replicate, '\n',
				    	'Comment: ', Comment, '\n',
				    	'SPM: ', 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 

```{r}
Ap_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Ap_532,
				    text=~paste0('Station: ', Station, '
',
				    	'ID: ', ID, '\n',
				     'SID: ', SID, '\n',
				    	'Replicate: ', Replicate, '\n',
				    	'Comment: ', Comment, '\n',
				    	'SPM: ', 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 

```{r SPM vs Bbp, echo=FALSE, message=FALSE}
Bbp_SPM_plot <- plot_ly(GLOB_sd, x=~SPM, y=~Bbp_532,
				    text=~paste0('Station: ', Station, '
',
				    	'ID: ', ID, '\n',
				     'SID: ', SID, '\n',
				    	'Replicate: ', Replicate, '\n',
				    	'Comment: ', Comment, '\n',
				    	'SPM: ', 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
```