api,plotting: Fix save all glitch

* R/api.R (create_plots): Fixed argument to single plot saving function.

* R/plotting.R <saving plots>: Clean up.

DESCRIPTION

 Package: shinyscreen
 Title: Pre-screening of Mass Spectrometry Data 
-Version: 1.0.0
+Version: 1.0.1
 Author: Todor Kondić
 Maintainer: Todor Kondić <todor.kondic@uni.lu>
 Authors@R: 

R/api.R

@@ -573,6 +573,11 @@ create_plots <- function(m) {
         pdata_ms2 <- data4plot_ms2_cgram(ms2,select)
         pdata_spec <- data4plot_ms2_spec(ms2,flt_summ,select)
 
+        tabl_ms1 <- table_eic(pdata_ms1)
+        ## tabl_ms2 <- table_eic(pdata_ms2) # For the moment, no real
+                                            # info to be had here.
+        tabl_spec <- table_spec(pdata_spec)
+
         palette = plot_palette(pdata_ms1)
 
         p_eic <- plot_eic_w_facet(pdata_ms1 = pdata_ms1,
@@ -584,18 +589,19 @@ create_plots <- function(m) {
                                     mz_range = c(NA_real_,NA_real_),
                                     palette = palette)
 
-        message("CCC")
+        ## TODO
         plot_save_single(p_eic,
                          decotab = select,
                          figtag = "eic",
                          proj = m$conf$project,
+                         tabl = tabl_ms1,
                          extension = m$conf$figures$ext)
 
-        message("DDD")
         plot_save_single(p_spec,
                          decotab = select,
                          figtag = "spec",
                          proj = m$conf$project,
+                         tabl = tabl_spec,
                          extension = m$conf$figures$ext)
         message("Plotting of figure ",n," out of ",NROW(keytab)," has been completed.")
         

R/plotting.R

@@ -282,9 +282,8 @@ table_spec <- function(pdata) {
     tbl
 }
 
-plot_save_single <- function(plot,decotab,extension,proj,tabl,figtag="") {
-    if (is.null(plot)) return()
-    print(decotab)
+plot_fname_prefix <- function(decotab,proj) {
+    if (NROW(decotab)==0) return()
     adducts <- decotab[,adduct]
     ids <- decotab[,ID]
     rpls <- list("\\["="","\\]"="","\\+"="p","\\-"="m")
@@ -302,6 +301,14 @@ plot_save_single <- function(plot,decotab,extension,proj,tabl,figtag="") {
     fname <- paste0(fname,paste(ids,collapse = "_"))
 
     fname <- file.path(ddir,fname)
+    fname
+    
+}
+
+plot_save_single <- function(plot,decotab,extension,proj,tabl=NULL,figtag="") {
+    if (is.null(plot)) return()
+
+    fname <- plot_fname_prefix(decotab,proj)
     
     fnplot <- paste0(fname,"__",figtag,".",extension)
 
@@ -311,7 +318,7 @@ plot_save_single <- function(plot,decotab,extension,proj,tabl,figtag="") {
                            plot = plot)
 
     fntab <- paste0(fname,"__",figtag,".csv")
-    data.table::fwrite(tabl,file=fntab,sep = ",")
+    if (! is.null(tabl)) data.table::fwrite(tabl,file=fntab,sep = ",")
 
 
 }