diff --git a/NAMESPACE b/NAMESPACE
index b7bd3fd4603ce3137e90e7101f1277782ac78144..658ae9e9b80c2940151e41788c73e2a2227e813c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,6 +11,7 @@ export(get_fn_conf)
export(get_fn_extr)
export(get_fn_ftab)
export(get_fn_summ)
+export(grab_unit)
export(launch)
export(list2rev)
export(load_compound_input)
diff --git a/R/api.R b/R/api.R
index feb653eafef7a36ac14a0ab57a6c9855fac6a4c0..39e54934cd407095d6f06a94402c0dd94f6a7b32 100644
--- a/R/api.R
+++ b/R/api.R
@@ -500,7 +500,6 @@ create_plots <- function(m) {
y <- m$out$tab$flt_summ
-
## Logarithmic, or linear y axis?
scale_y_ms1_eic <- if (shiny::isTruthy(m$conf$logaxes$ms1_eic_int))
ggplot2::scale_y_log10 else ggplot2::scale_y_continuous
@@ -511,6 +510,8 @@ create_plots <- function(m) {
scale_y_ms2_spec <- if (shiny::isTruthy(m$conf$logaxes$ms2_spec_int))
ggplot2::scale_y_log10 else ggplot2::scale_y_continuous
+ scale_x <- function(...) ggplot2::scale_x_continuous(...,limits=DEFAULT_RT_RANGE)
+
## Colour palette.
tags <- y[,unique(tag)]
getpal <- colorRampPalette(RColorBrewer::brewer.pal(8,"Dark2"))
@@ -518,10 +519,10 @@ create_plots <- function(m) {
names(col_all_vals) <- tags
scale_colour <- function(values=col_all_vals,...) ggplot2::scale_colour_manual(values = values,name=m$conf$figures[["legend title"]],...)
-
- rt_lim <- DEFAULT_RT_RANGE
- if (!is.null(m$conf$figures$rt_min)) rt_lim[[1]] <- m$conf$figures$rt_min
- if (!is.null(m$conf$figures$rt_max)) rt_lim[[2]] <- m$conf$figures$rt_max
+ rt_new_lim <- c(rt_in_min(m$conf$figures$rt_min),
+ rt_in_min(m$conf$figures$rt_max))
+ rt_lim <- get_coord_lim(rt_new_lim,DEFAULT_RT_RANGE)
+
my_coord <- ggplot2::coord_cartesian(xlim = rt_lim)
conf_psub <- m$conf$figures[["plot subset"]]
@@ -556,6 +557,7 @@ create_plots <- function(m) {
) +
scale_y_ms1_eic(labels=sci10) +
scale_colour(values=col_all_vals[as.character(tags)]) +
+ scale_x() +
my_coord +
my_theme()
}
@@ -574,6 +576,7 @@ create_plots <- function(m) {
) +
scale_y_ms2_eic(labels=sci10) +
scale_colour(values=col_all_vals[as.character(ddf$tag)]) +
+ scale_x() +
my_coord +
my_theme()
}
@@ -602,6 +605,7 @@ create_plots <- function(m) {
## title=mk_title("MS2 spectrum for precursor",mz)
) +
scale_y_ms2_spec(labels=sci10) +
+ scale_x() +
scale_colour(values=col_all_vals[as.character(tags)]) +
my_theme()
}
@@ -671,8 +675,8 @@ save_plots <- function(m) {
dir.create(topdir,showWarnings = F)
rt_lim <- DEFAULT_RT_RANGE
- if (!is.null(m$conf$figures$rt_min)) rt_lim[[1]] <- m$conf$figures$rt_min
- if (!is.null(m$conf$figures$rt_max)) rt_lim[[2]] <- m$conf$figures$rt_max
+ if (isTruthy(m$conf$figures$rt_min)) rt_lim[[1]] <- rt_in_min(m$conf$figures$rt_min)
+ if (isTruthy(m$conf$figures$rt_max)) rt_lim[[2]] <- rt_in_min(m$conf$figures$rt_max)
my_theme <- function(...) ggplot2::theme(legend.position = "none",...)
@@ -695,6 +699,7 @@ save_plots <- function(m) {
ids <- asdf[,unique(ID)]
for (id in ids) {
message("Image ","set: ",s," group: ", g, " id: ",id)
+
tab <- asdf[ID==id,.(tag,ms1_int,ms1_rt,adduct,mz)]
ms1_figs <- m$out$tab$ms1_plot_eic[set==s & adduct==g & ID==id,.(fig,structfig)]
ms2_figs <- m$out$tab$ms2_plot[set==s & adduct==g & ID==id,.(fig_eic,fig_spec)]
diff --git a/R/mix.R b/R/mix.R
index f0268b7f4cf94b66ef0bc5fa8d992d30299410cc..233fa46bb29eb62cb8deb69175a980b984e04e0e 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -819,6 +819,8 @@ verify_cmpd_l <- function(dt,fn) {
## INPUT TRANSLATORS
+
+#' @export
grab_unit <- function(entry,unit) {
what <- paste0("\\<",unit,"\\>$")
entry <- trimws(entry,which="both")
@@ -827,6 +829,13 @@ grab_unit <- function(entry,unit) {
}
+rt_in_min <- function(entry) {
+ xs <- grab_unit(entry,"s")
+ xm <- grab_unit(entry,"min")
+ x <- if (is.na(xm)) xs/60. else xm
+ x
+}
+
conf_trans_pres <- function(pres_list) {
## Translate and validate prescreening input.
pres_list[CONF_PRES_NUM] <- sapply(pres_list[CONF_PRES_NUM],as.numeric)
@@ -1028,3 +1037,11 @@ fig_path <- function(top,set,group,id,suff,ext="pdf") {
fn <- gsub("-","m",fn)
if (!is.null(top)) file.path(top,fn) else fn
}
+
+get_coord_lim <- function(new,def) {
+ if (is.null(new)) return(def)
+ res <- new
+ if (length(new[[1]])==0) res[[1]]<-def[[1]]
+ if (length(new[[2]])==0) res[[2]]<-def[[2]]
+ res
+}
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 7d359e1eeb5edc465bab495132e8eca6aa98ebbe..661ba0da97e815a5b8257d59eeab70dd695e96e6 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -291,7 +291,7 @@ Filter entries in the summary table according to the QA criteria.
For those who do not speak Italian (and do not dig the bad Sergio
Leone pun):
-* **il irrelevante** : ignore QA criterion
+* **l'irrelevante** : ignore QA criterion
* **il buono** : entry passed QA
* **il cattivo** : entry failed QA
@@ -442,6 +442,57 @@ DT::dataTableOutput("summ_table")
# Browse Results
+Generate plots.
+
+```{r, echo=F}
+
+uiOutput("plot_b_ctrl")
+
+```
+<div style="display: flex; ">
+
+<div>
+```{r, echo=F}
+
+uiOutput("plot_set_b_ctrl")
+
+## selectInput(inputId = "plot_set_b",
+## label = "Select set",
+## choices = c("uninitialised"=0))
+```
+</div>
+
+<div style="vertical-align: bottom; ">
+```{r, echo=F}
+
+uiOutput("plot_id_b_ctrl")
+## selectInput(inputId = "plot_id_b",
+## label = "Select ID",
+## choices = c("uninitialised"=0))
+```
+</div>
+
+</div>
+
+
+<div style="display: flex; ">
+
+<div style="vertical-align: bottom; ">
+```{r, echo=F}
+actionButton(inputId = "plot_next_b",
+ label = "Previous")
+```
+</div>
+
+<div style="vertical-align: bottom; ">
+```{r, echo=F}
+actionButton(inputId = "plot_prev_b",
+ label = "Next")
+```
+</div>
+
+
+</div>
<!-- ENGINE -->
@@ -801,6 +852,26 @@ observeEvent(input$presc_b,{
})
+observeEvent(input$plot_b,{
+ validate(need(NROW(rv_state$out$tab$flt_summ) > 0,
+ message = "Perform prescreening first."))
+ m <- rev2list(rv_state)
+
+ fn_c_state <- file.path(m$conf$project,
+ paste0("genplot.",shinyscreen:::FN_CONF))
+ yaml::write_yaml(x=m$conf,file=fn_c_state)
+ message("(generate plots) Config written to ", fn_c_state)
+ state <- withr::with_dir(new=m$conf$project,
+ code = {
+ m <- create_plots(m)
+ save_plots(m)
+ })
+ message("(generate plots) Done generating plots.")
+
+ z <- shinyscreen::merge2rev(rv_state,lst = state)
+ eval(z)
+})
+
observeEvent(input$conf_file_save_b,
{
state <- rf_conf_state()
@@ -1015,9 +1086,12 @@ output$summ_subset <- rhandsontable::renderRHandsontable({
output$summ_table <- DT::renderDataTable({
- tab <- rv_state$out$tab$flt_summ[,.(Files=NULL)]
+
+ tab <- rv_state$out$tab$flt_summ
+ nms <- colnames(tab)
+ dpl_nms <- nms[nms!="Files"]
validate(need(NROW(tab)>0, message = "Please prescreen the data first."))
- DT::datatable(tab,
+ DT::datatable(tab[,..dpl_nms],
style = 'bootstrap',
class = 'table-condensed',
extensions = 'Scroller',
@@ -1026,8 +1100,23 @@ output$summ_table <- DT::renderDataTable({
deferRender = T,
scroller = T))
})
-```
+output$plot_set_b_ctrl <- renderUI({
+ tab <- rv_state$out$tab$flt_summ
+ req(NROW(tab)>0)
+ selectInput(inputId = "plot_set_b",
+ label = "Select set",
+ choices = c("uninitialised"=0))
+})
+
+output$plot_b_ctrl <- renderUI({
+ tab <- rv_state$out$tab$flt_summ
+ req(NROW(tab)>0)
+ actionButton(inputId = "plot_b",
+ label= "Generate plots")
+
+})
+```
```{r, echo=F, context = 'server'}