diff --git a/R/mix.R b/R/mix.R
index e1afbcd328639d47e753a4c61f3f470376124a9c..5d8ce29a0e33a102e42e986ba58e25098c947346 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -326,18 +326,6 @@ preProc <- function (summ,noiseFac=3,errRT=0.5,intThreshMS1=1e5,intThreshMS2=500
summ
}
-smiles2img <- function(smiles, kekulise=TRUE, width=300, height=300,
- zoom=1.3,style="cow", annotate="off", abbr="on",suppressh=TRUE,
- showTitle=FALSE, smaLimit=100, sma=NULL) {
- dep <- rcdk::get.depictor(width = width, height = height, zoom = zoom, style = style, annotate = annotate,
- abbr = abbr, suppressh = suppressh, showTitle = showTitle, smaLimit = smaLimit,
- sma = NULL)
-
- mol <- RMassBank::getMolecule(smiles)
- z<-rcdk::view.image.2d(mol, depictor=dep)
- grid::rasterGrob(z)
-}
-
gen_ms2_spec_data <- function(id,tag,iMS2rt,data,luckyN=NA) {
## Given the id, tag and the index of the MS2 spectrum, return the
## dataframe of the spectrum, with luckyN number of lagerst
diff --git a/R/plotting.R b/R/plotting.R
index 7d203b3557ef6e9a1499cb80ca7928980b46126f..01529c55924ea9a26883e120c8b663729d539cd8 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -339,6 +339,17 @@ plot_save_single <- function(plot,decotab,extension,proj_path,subdir=FIG_TOPDIR,
## NEW BEGINNINGS
+smiles2img <- function(smiles, kekulise=TRUE, width=300, height=300,
+ zoom=1.3,style="cow", annotate="off", abbr="on",suppressh=TRUE,
+ showTitle=FALSE, smaLimit=100, sma=NULL) {
+ dep <- rcdk::get.depictor(width = width, height = height, zoom = zoom, style = style, annotate = annotate,
+ abbr = abbr, suppressh = suppressh, showTitle = showTitle, smaLimit = smaLimit,
+ sma = NULL)
+
+ mol <- RMassBank::getMolecule(smiles)
+ z<-rcdk::view.image.2d(mol, depictor=dep)
+ grid::rasterGrob(z)
+}
theme_eic <- function(...) theme_light()+ggplot2::theme(axis.title=ggplot2::element_text(size=15L),
axis.text=ggplot2::element_text(size=12L,colour="black"),
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index f2bf6ae59387c8e8213b19475bdc28980959834b..e93fa9ae54dccefc41b0847c7f59be7277fb0384 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1276,8 +1276,22 @@ mk_shinyscreen_server <- function(projects,init) {
p3 <- rf_plot_spec_ms2()
combine_plots(p1,p2,p3)
+
},height=1000)
+ output$plot_hover_out <- renderText({
+ inp1 <- input$plot_hover[[1]]
+ inp2 <- input$plot_hover[[2]]
+ res <- if (all(!(c(is.null(inp1),is.null(inp2))))) {
+ paste0('(',
+ format(inp1,digits=5),
+ ',',
+ format(inp2,digits=2,scientific=T),
+ ')')
+ } else "Currently not in the plot."
+
+ })
+
output$plot_struct <- renderPlot({
rf_plot_struct()
})
@@ -2007,18 +2021,7 @@ mk_shinyscreen_server <- function(projects,init) {
rf_plot_spec_facet()
})
- output$plot_hover_out <- renderText({
- inp1 <- input$plot_hover[[1]]
- inp2 <- input$plot_hover[[2]]
- res <- if (all(!(c(is.null(inp1),is.null(inp2))))) {
- paste0('(',
- format(inp1,digits=5),
- ',',
- format(inp2,digits=2,scientific=T),
- ')')
- } else "Currently not in the plot."
-
- })
+
output$dwn_proj_b <- shiny::downloadHandler(
filename=function() {
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 67e0740f4ce12ba160fc45f4ed4c14449963bf32..1ebb857e743f68617a44791faff6c7fc061cd43a 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -614,13 +614,17 @@ DT::dataTableOutput("setid_table")
<div style="display: flex; flex-flow: column; padding-right:1.0em">
### Compound Index
```{r, echo=F}
-selectInput("cindex_group",label="Group",choices=c(NA_character_,"adduct","tag"), multiple=T)
+selectInput("cindex_group",label="Group",
+ choices=c(NA_character_,
+ "adduct","tag"),
+ multiple=T,
+ selected=c("adduct","tag"))
```
<div style="display: flex; flex-flow: row nowrap">
```{r, echo=F}
-selectInput("sort1",label="Sort by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
-selectInput("sort2",label="then by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
+selectInput("sort1",label="Sort by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%",selected="quality")
+selectInput("sort2",label="then by ", choices=shinyscreen:::ARRANGE_CHOICES,width="15%",selected="mz")
selectInput("sort3",label="then", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
selectInput("sort4",label="and finally by", choices=shinyscreen:::ARRANGE_CHOICES,width="15%")
```
@@ -640,25 +644,6 @@ DT::DTOutput("cindex")
<div style="display: flex; flex-direction: row; flex-wrap: nowrap;"> <!-- EICs and Structure -->
<div style="width: 80%; overflow-y: scroll;"> <!-- EIC ID Plot -->
```{r,echo=F}
-## plotOutput("plot_eic_ms1",
-## hover = hoverOpts(id="plot_hover",
-## delayType = "throttle",
-## delay=100),
-## dblclick = "plot_rt_click",
-## brush = "plot_brush")
-## plotOutput("plot_eic_ms2",
-## hover = hoverOpts(id="plot_hover",
-## delayType = "throttle",
-## delay=100),
-## dblclick = "plot_rt_click",
-## brush = "plot_brush")
-## plotOutput("plot_spec_ms2",
-## hover = hoverOpts(id="plot_hover",
-## delayType = "throttle",
-## delay=100),
-## dblclick = "plot_mz_click",
-## brush = brushOpts(id="plot_mz_brush"))
-
plotOutput("plot_eic_combined",
## height="100%",
hover = hoverOpts(id="plot_hover",
@@ -669,24 +654,24 @@ plotOutput("plot_eic_combined",
```
</div> <!-- EIC ID Plot -->
-<div style="width: 20%;"> <!-- Structure -->
+<div style="display: flex; flex-direction: column; width=20%;"> <!-- Structure and Dynamic Plot Data -->
+
```{r, echo=F}
-plotOutput("plot_struct")
+plotOutput("plot_struct", width="400%")
```
-</div> <!-- Structure -->
+
+#### Pointer Position
+
+```{r, echo=F}
+textOutput("plot_hover_out")
+```
+
+</div> <!-- Structure and Dynamic Plot Data -->
+
</div> <!-- EICs and Structure -->
<div style="display: flex; flex-direction: row; flex-wrap: nowrap;"> <!-- Spec and Details-->
-<!-- <div style="width: 40%"> <\!-- MS2 Spec -\-> -->
-<!-- ```{r, echo=F} -->
-<!-- plotOutput("plot_spec_ms2", -->
-<!-- hover = hoverOpts(id="plot_hover", -->
-<!-- delayType = "throttle", -->
-<!-- delay=100), -->
-<!-- dblclick = "plot_mz_click", -->
-<!-- brush = brushOpts(id="plot_mz_brush")) -->
-<!-- ``` -->
-<!-- </div> <\!-- MS2 Spec -\-> -->
+
<div style="display: flex; flex-direction: row; flex-wrap: nowrap; padding-top: 2em; padding-left: 2em;"> <!-- Modification -->
<div> <!-- Select MS1 curve -->
```{r,echo=F}
@@ -707,11 +692,6 @@ actionButton(inputId="change_qa_b",label="Commit changes")
</div> <!-- Spec and Details-->
<div style="display: flex-flow: row nowrap"> <!-- Control Bar -->
-
-```{r,echo=F}
-textOutput("plot_hover_out")
-```
-
```{r, echo=F}
actionButton("plot_save_single",
label="Save this plot")