From a8f6e87c003b1e010eee9ddbaa735ce2a0e20dc4 Mon Sep 17 00:00:00 2001
From: Maciej Dobrzynski <maciekd@izbherat.unibe.ch>
Date: Mon, 27 May 2019 18:16:45 +0200
Subject: [PATCH] Bug fixes

---
 modules/auxfunc.R | 39 +++++++++++++++++++++++----------------
 server.R          |  6 +++---
 ui.R              |  2 +-
 3 files changed, 27 insertions(+), 20 deletions(-)

diff --git a/modules/auxfunc.R b/modules/auxfunc.R
index 8ceb1f2..3a80d81 100644
--- a/modules/auxfunc.R
+++ b/modules/auxfunc.R
@@ -19,14 +19,21 @@ require(Hmisc) # for CI calculation
 DEB = T
 
 # font sizes in pts for plots
-PLOTFONTBASE = 8
-PLOTFONTAXISTEXT = 8
-PLOTFONTAXISTITLE = 8
-PLOTFONTFACETSTRIP = 10
-PLOTFONTLEGEND = 8
+# PLOTFONTBASE = 8
+# PLOTFONTAXISTEXT = 8
+# PLOTFONTAXISTITLE = 8
+# PLOTFONTFACETSTRIP = 10
+# PLOTFONTLEGEND = 8
+
+PLOTFONTBASE = 12
+PLOTFONTAXISTEXT = 12
+PLOTFONTAXISTITLE = 12
+PLOTFONTFACETSTRIP = 16
+PLOTFONTLEGEND = 12
+
 
 # default number of facets in plots
-PLOTNFACETDEFAULT = 3
+PLOTNFACETDEFAULT = 2
 
 # internal column names
 COLRT   = 'realtime'
@@ -229,20 +236,20 @@ LOCgenTraj <- function(in.ntpts = 60, in.ntracks = 10, in.nfov = 6, in.nwells =
   # add outliers for testing
   if (!is.null(in.addout)) {
     locTabLen = length(x.rand.1)
-    x.rand.1[round(runif(in.addout) * locTabLen)] = 10
-    x.rand.2[round(runif(in.addout) * locTabLen)] = 10
+    x.rand.1[round(runif(in.addout) * locTabLen)] = 5
+    x.rand.2[round(runif(in.addout) * locTabLen)] = 5
   }
   
   x.arg = rep(seq(1, in.ntpts), in.ntracks * in.nfov)
   
-  dt.nuc = data.table(Metadata_Well = rep(LETTERS[1:in.nwells], each = in.ntpts * in.nfov * in.ntracks / in.nwells),
-                      Metadata_Site = rep(1:in.nfov, each = in.ntpts * in.ntracks),
-                      Metadata_RealTime = x.arg,
-                      objCyto_Intensity_MeanIntensity_imErkCor = x.rand.1,
-                      objNuc_Intensity_MeanIntensity_imErkCor  = x.rand.2,
-                      objNuc_Location_X = runif(in.ntpts * in.ntracks * in.nfov, min = 0, max = 1),
-                      objNuc_Location_Y = runif(in.ntpts * in.ntracks * in.nfov, min = 0, max = 1),
-                      TrackLabel = rep(1:(in.ntracks*in.nfov), each = in.ntpts))
+  dt.nuc = data.table(well = rep(LETTERS[1:in.nwells], each = in.ntpts * in.nfov * in.ntracks / in.nwells),
+                      group = rep(1:in.nfov, each = in.ntpts * in.ntracks),
+                      time = x.arg,
+                      y1 = x.rand.1,
+                      y2  = x.rand.2,
+                      posx = runif(in.ntpts * in.ntracks * in.nfov, min = 0, max = 1),
+                      posy = runif(in.ntpts * in.ntracks * in.nfov, min = 0, max = 1),
+                      id = rep(1:(in.ntracks*in.nfov), each = in.ntpts))
   
   return(dt.nuc)
 }
diff --git a/server.R b/server.R
index ae78d82..c31e0f6 100644
--- a/server.R
+++ b/server.R
@@ -241,7 +241,7 @@ shinyServer(function(input, output, session) {
     
     if (input$chBtrackUni) {
       locCols = getDataNucCols()
-      locColSel = locCols[grep('(S|s)ite|(S|s)eries|(F|f)ov', locCols)[1]] # index 1 at the end in case more matches; select 1st
+      locColSel = locCols[grep('(S|s)ite|(S|s)eries|(F|f)ov|(G|g)roup', locCols)[1]] # index 1 at the end in case more matches; select 1st
       
       selectInput(
         'inSelSite',
@@ -261,7 +261,7 @@ shinyServer(function(input, output, session) {
     locCols = getDataNucCols()
     
     if (!is.null(locCols)) {
-      locColSel = locCols[grep('(R|r)atio|(I|i)ntensity|y|Meas', locCols)[1]] # index 1 at the end in case more matches; select 1st
+      locColSel = locCols[grep('(R|r)atio|(I|i)ntensity|(Y|y)|(M|m)eas', locCols)[1]] # index 1 at the end in case more matches; select 1st
 
       selectInput(
         'inSelMeas1',
@@ -282,7 +282,7 @@ shinyServer(function(input, output, session) {
     
     if (!is.null(locCols) &&
         !(input$inSelMath %in% c('', '1 / '))) {
-      locColSel = locCols[grep('(R|r)atio|(I|i)ntensity|y|Meas', locCols)[1]] # index 1 at the end in case more matches; select 1st
+      locColSel = locCols[grep('(R|r)atio|(I|i)ntensity|(Y|y)|(M|m)eas', locCols)[1]] # index 1 at the end in case more matches; select 1st
 
       selectInput(
         'inSelMeas2',
diff --git a/ui.R b/ui.R
index 1cabee9..7f801d4 100644
--- a/ui.R
+++ b/ui.R
@@ -64,7 +64,7 @@ shinyUI(fluidPage(
       uiOutput('varSelTime'),
       uiOutput('varSelMeas1'),
       radioButtons(
-        'inSelMath', width = '25%',
+        'inSelMath', width = '50%',
         'Math on 1st and 2nd meas.:',
         c(
           'None' = '',
-- 
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