Misc. tweaks to interface

ppernot · Mar 23, 2023 · e81de28 · e81de28
1 parent ff8af0d
commit e81de28
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Showing 10 changed files with 92 additions and 48 deletions.
diff --git a/R/graphFuncs.R b/R/graphFuncs.R
@@ -1036,16 +1036,17 @@ plotMS <- function(
   text.cex = 1) {
 
   plot(x, y, type = 'n',
-       xlim = xlim, xlab = xlab, cex.axis=0.75,
+       xlim = xlim, xlab = xlab, cex.axis=0.75, xaxt = 'n',
        ylim = ylim, ylab = 'Mole fraction', yaxs ='i',
        main = main)
 
   # Axis
-  if(diff(range(xlim)) <= 20)
+  if(diff(range(xlim)) <= 20) {
     step = 1
-  else
+  } else {
     step = 5
-  ti = seq(floor(xlim[1]), ceiling(xlim[2]), by = step)
+  }
+  ti = seq(floor(xlim[1]/step)*step, ceiling(xlim[2]/step)*step, by = step)
   axis(side = 1, at = ti, labels = ti, cex.axis=0.75)
   grid()
 

diff --git a/global.R b/global.R
@@ -1,3 +1,5 @@
+version = 1.5
+
 # Options ####
 Sys.setlocale(
   category = "LC_NUMERIC",

diff --git a/server_files/analysis.R b/server_files/analysis.R
@@ -381,7 +381,8 @@ generateCategories = function(species) {
   radic[is.na(radic)] = 0
 
   ## Define species groups according to composition
-  grp = rep('Misc.',length(species))
+  lnk = '.'
+  grp = rep('Dummy',length(species))
   sel = colSums(compo) != 0
   ns  = sum(sel)
   elt = elements[sel]
@@ -398,7 +399,7 @@ generateCategories = function(species) {
         e2 = elt[j]
         sel = cop[,i] & cop[,j]
         if(any(sel))
-          grp[sel] = paste0(e1,'&',e2)
+          grp[sel] = paste0(e1,lnk,e2)
       }
     }
   if(ns >= 3)
@@ -410,7 +411,7 @@ generateCategories = function(species) {
           e3 = elt[k]
           sel = cop[,i] & cop[,j] & cop[,k]
           if(any(sel))
-            grp[sel] = paste0(e1,'&',e2,'&',e3)
+            grp[sel] = paste0(e1,lnk,e2,lnk,e3)
         }
       }
     }
@@ -425,23 +426,23 @@ generateCategories = function(species) {
             e4 = elt[l]
             sel = cop[,i] & cop[,j] & cop[,k] & cop[,l]
             if(any(sel))
-              grp[sel] = paste0(e1,'&',e2,'&',e3,'&',e4)
+              grp[sel] = paste0(e1,lnk,e2,lnk,e3,lnk,e4)
           }
         }
       }
     }
 
   ## Mass
   mass = apply(compo, 1, massFormula)
-  if(any(species %in% spDummy)){
-    dummyMass   = round(max(mass,na.rm=TRUE) + 2 )
+  if (any(species %in% spDummy)) {
+    dummyMass   = round(max(mass, na.rm = TRUE) + 2)
     mass[species %in% spDummy] = dummyMass
   }
 
   ## Nb of heavy atoms
   nbh = nbHeavyAtoms(species)
-  if(any(species %in% spDummy))
-    nbh[species %in% spDummy] = max(nbh) + 1
+  if (any(species %in% spDummy))
+    nbh[species %in% spDummy] = max(nbh, na.rm = TRUE) + 2
   # nbh[is.na(nbh)] = 0
 
   list(
@@ -636,7 +637,7 @@ output$categsPlot <- renderUI({
   ui = list(
     br(),
     strong("Selection"),
-    hr(style="border-color: #666;")
+    hr()
   )
   ii = 3
 
@@ -837,7 +838,7 @@ req(speciesCategories())
 ui = list(
   br(),
   strong("Selection"),
-  hr(style="border-color: #666;")
+  hr()
 )
 ii = 3
 

diff --git a/server_files/model.R b/server_files/model.R
@@ -510,7 +510,8 @@ setGroups = function(species, netColoring, vlpI) {
 
   } else if (netColoring == 'compo') {
     # Define species groups according to composition
-    grp = rep('Misc.',length(species))
+    lnk = '.'
+    grp = rep('Dummy',length(species))
     sel = colSums(compo) != 0
     ns  = sum(sel)
     elt = elements[sel]
@@ -527,7 +528,7 @@ setGroups = function(species, netColoring, vlpI) {
           e2 = elt[j]
           sel = cop[,i] & cop[,j]
           if(any(sel))
-            grp[sel] = paste0(e1,'&',e2)
+            grp[sel] = paste0(e1,lnk,e2)
         }
       }
     if(ns >= 3)
@@ -539,7 +540,7 @@ setGroups = function(species, netColoring, vlpI) {
             e3 = elt[k]
             sel = cop[,i] & cop[,j] & cop[,k]
             if(any(sel))
-              grp[sel] = paste0(e1,'&',e2,'&',e3)
+              grp[sel] = paste0(e1,lnk,e2,lnk,e3)
           }
         }
       }
@@ -554,16 +555,17 @@ setGroups = function(species, netColoring, vlpI) {
               e4 = elt[l]
               sel = cop[,i] & cop[,j] & cop[,k] & cop[,l]
               if(any(sel))
-                grp[sel] = paste0(e1,'&',e2,'&',e3,'&',e4)
+                grp[sel] = paste0(e1,lnk,e2,lnk,e3,lnk,e4)
             }
           }
         }
       }
 
   }  else if (netColoring == 'mass') {
     nbh = nbHeavyAtoms(species)
-    nbh[is.na(nbh)] = 0
-    grp = paste0('C',nbh)
+    nbh[species %in% spDummy] = max(nbh, na.rm = TRUE) + 2
+    # nbh[is.na(nbh)] = 0
+    grp = nbh
 
   }
   return(grp)

diff --git a/ui.R b/ui.R
@@ -11,6 +11,13 @@ function(request) {
     theme = shinythemes::shinytheme(
       c("cosmo", "cerulean", "spacelab", "yeti")[3]
     ),
+    tags$head(tags$style(HTML("
+      hr {
+        height: 1px;
+        margin-top: 0.0em;
+        background: #666;
+      }"
+    ))),
     tabPanel(
       title = "Project",
       source_ui("project.R")
@@ -30,14 +37,14 @@ function(request) {
     tabPanel(
       title = "Fluxes",
       source_ui("fluxes.R")
-    ),
+    )#,
     # tabPanel(
     #   title = "Downloads",
     #   source_ui("downloads.R")
     # ),
-    tabPanel(
-      title = "About",
-      source_ui("about.R")
-    )
+    # tabPanel(
+    #   title = "About",
+    #   source_ui("about.R")
+    # )
   )
 }
diff --git a/ui_files/about.R → ui_files/about.Rold b/ui_files/about.R → ui_files/about.Rold
diff --git a/ui_files/analysis.R b/ui_files/analysis.R
@@ -68,6 +68,11 @@ sidebarLayout(
             column(
               width = 3,
               wellPanel(
+                uiOutput(
+                  "categsPlot"
+                ),
+                strong("Plot"),
+                hr(),
                 checkboxInput(
                   "mcPlot",
                   "Show error bands",
@@ -87,9 +92,6 @@ sidebarLayout(
                   "ppscale",
                   "Draw PPM scale",
                   value = FALSE
-                ),
-                uiOutput(
-                  "categsPlot"
                 )
               )
             ),
@@ -117,6 +119,11 @@ sidebarLayout(
             column(
               width = 3,
               wellPanel(
+                uiOutput(
+                  "categsPlotMS"
+                ),
+                strong("Plot"),
+                hr(),
                 checkboxInput(
                   "mcPlotMS",
                   "Show error bars",
@@ -127,9 +134,6 @@ sidebarLayout(
                   "Draw PPM scale",
                   value = FALSE
                 ),
-                uiOutput(
-                  "categsPlotMS"
-                ),
                 sliderInput(
                   "timeMS",
                   "Log sampling time",
@@ -183,6 +187,28 @@ sidebarLayout(
             column(
               width = 3,
               wellPanel(
+                fluidRow(
+                  column(6,
+                         textInput(
+                           "SASpecies",
+                           "Target",
+                           width = "100%",
+                           value = NULL,
+                           placeholder = "Species"
+                         )
+                  ),
+                  column(6,
+                         actionButton(
+                           'doSA',
+                           'Run SA',
+                           icon = icon('gear')
+                         ),
+                         tags$style(
+                           type = 'text/css',
+                           "#doSA { width:100%; margin-top: 27px;}"
+                         )
+                  )
+                ),
                 radioButtons(
                   "anaType",
                   "Sensitivity indices",
@@ -192,19 +218,6 @@ sidebarLayout(
                     "dHSIC"        = "hsic"
                   )
                 ),
-                textInput(
-                  "SASpecies",
-                  "Choose species",
-                  width = "50%",
-                  value = NULL,
-                  placeholder = "Type species"
-                ),
-                actionButton(
-                  'doSA',
-                  'Run SA',
-                  icon = icon('gear')
-                ),
-                hr(),
                 radioButtons(
                   "SAPlotType",
                   "Plot Type",

diff --git a/ui_files/model.R b/ui_files/model.R
@@ -2,7 +2,7 @@ sidebarLayout(
   sidebarPanel(
     width = sideWidth,
     h4("Model control"),
-    hr( style="border-color: #666;"),
+    # hr( style="border-color: #666;"),
     verbatimTextOutput("contentsNmlMsg")
   ),
   mainPanel(
@@ -84,7 +84,7 @@ sidebarLayout(
                       'netColoring',
                       'Color scheme',
                       choiceNames = list(
-                        'Volpert','Charge','Radicals','Composition','Mass'
+                        'Volpert','Charge','Radicals','Composition','Heavy atoms'
                       ),
                       choiceValues = list(
                         'volpert','charge','radicals','compo','mass'

diff --git a/ui_files/project.R b/ui_files/project.R
@@ -34,7 +34,25 @@ sidebarLayout(
           'Save Project',
           icon = icon('gear')
         )
-
+      ),
+      br(),br(),br(),
+      wellPanel(
+        h4("About"),
+        hr(),
+        h5("Author      : P. Pernot"),
+        h5("Affiliation : ",a(href="https://www.cnrs.fr/","CNRS")),
+        h5(paste0("Version     : ",version)),
+        # h5("Date        : 2022/09/19"),
+        br(),
+        a(href="https://github.com/ppernot/ReactorUI","How to cite..."),
+        br(),
+        a(href="https://github.com/ppernot/ReactorUI","code@github"),
+        br(),
+        a(href="https://github.com/ppernot/ReactorUI/issues",
+          "Bugs report, Features request"),
+        br(),
+        a(href="https://ppernot.github.io/ReactorUI",
+          "User's manual")
       )
     )
   ),

diff --git a/ui_files/run.R b/ui_files/run.R
@@ -2,7 +2,7 @@ sidebarLayout(
   sidebarPanel(
     width = sideWidth,
     h4("Run Reactor"),
-    hr( style="border-color: #666;"),
+    hr(),
     uiOutput("nMCRunSelect"),
     tabsetPanel(
       tabPanel(