Commit a8f6e87c authored by Maciej Dobrzynski's avatar Maciej Dobrzynski

Bug fixes

parent 602f8b92
...@@ -19,14 +19,21 @@ require(Hmisc) # for CI calculation ...@@ -19,14 +19,21 @@ require(Hmisc) # for CI calculation
DEB = T DEB = T
# font sizes in pts for plots # font sizes in pts for plots
PLOTFONTBASE = 8 # PLOTFONTBASE = 8
PLOTFONTAXISTEXT = 8 # PLOTFONTAXISTEXT = 8
PLOTFONTAXISTITLE = 8 # PLOTFONTAXISTITLE = 8
PLOTFONTFACETSTRIP = 10 # PLOTFONTFACETSTRIP = 10
PLOTFONTLEGEND = 8 # PLOTFONTLEGEND = 8
PLOTFONTBASE = 12
PLOTFONTAXISTEXT = 12
PLOTFONTAXISTITLE = 12
PLOTFONTFACETSTRIP = 16
PLOTFONTLEGEND = 12
# default number of facets in plots # default number of facets in plots
PLOTNFACETDEFAULT = 3 PLOTNFACETDEFAULT = 2
# internal column names # internal column names
COLRT = 'realtime' COLRT = 'realtime'
...@@ -229,20 +236,20 @@ LOCgenTraj <- function(in.ntpts = 60, in.ntracks = 10, in.nfov = 6, in.nwells = ...@@ -229,20 +236,20 @@ LOCgenTraj <- function(in.ntpts = 60, in.ntracks = 10, in.nfov = 6, in.nwells =
# add outliers for testing # add outliers for testing
if (!is.null(in.addout)) { if (!is.null(in.addout)) {
locTabLen = length(x.rand.1) locTabLen = length(x.rand.1)
x.rand.1[round(runif(in.addout) * locTabLen)] = 10 x.rand.1[round(runif(in.addout) * locTabLen)] = 5
x.rand.2[round(runif(in.addout) * locTabLen)] = 10 x.rand.2[round(runif(in.addout) * locTabLen)] = 5
} }
x.arg = rep(seq(1, in.ntpts), in.ntracks * in.nfov) 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), dt.nuc = data.table(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), group = rep(1:in.nfov, each = in.ntpts * in.ntracks),
Metadata_RealTime = x.arg, time = x.arg,
objCyto_Intensity_MeanIntensity_imErkCor = x.rand.1, y1 = x.rand.1,
objNuc_Intensity_MeanIntensity_imErkCor = x.rand.2, y2 = x.rand.2,
objNuc_Location_X = runif(in.ntpts * in.ntracks * in.nfov, min = 0, max = 1), posx = 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), posy = runif(in.ntpts * in.ntracks * in.nfov, min = 0, max = 1),
TrackLabel = rep(1:(in.ntracks*in.nfov), each = in.ntpts)) id = rep(1:(in.ntracks*in.nfov), each = in.ntpts))
return(dt.nuc) return(dt.nuc)
} }
......
...@@ -241,7 +241,7 @@ shinyServer(function(input, output, session) { ...@@ -241,7 +241,7 @@ shinyServer(function(input, output, session) {
if (input$chBtrackUni) { if (input$chBtrackUni) {
locCols = getDataNucCols() 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( selectInput(
'inSelSite', 'inSelSite',
...@@ -261,7 +261,7 @@ shinyServer(function(input, output, session) { ...@@ -261,7 +261,7 @@ shinyServer(function(input, output, session) {
locCols = getDataNucCols() locCols = getDataNucCols()
if (!is.null(locCols)) { 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( selectInput(
'inSelMeas1', 'inSelMeas1',
...@@ -282,7 +282,7 @@ shinyServer(function(input, output, session) { ...@@ -282,7 +282,7 @@ shinyServer(function(input, output, session) {
if (!is.null(locCols) && if (!is.null(locCols) &&
!(input$inSelMath %in% c('', '1 / '))) { !(input$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( selectInput(
'inSelMeas2', 'inSelMeas2',
......
...@@ -64,7 +64,7 @@ shinyUI(fluidPage( ...@@ -64,7 +64,7 @@ shinyUI(fluidPage(
uiOutput('varSelTime'), uiOutput('varSelTime'),
uiOutput('varSelMeas1'), uiOutput('varSelMeas1'),
radioButtons( radioButtons(
'inSelMath', width = '25%', 'inSelMath', width = '50%',
'Math on 1st and 2nd meas.:', 'Math on 1st and 2nd meas.:',
c( c(
'None' = '', 'None' = '',
......
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