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pertz-lab
shiny-timecourse-inspector
Commits
a8f6e87c
Commit
a8f6e87c
authored
May 27, 2019
by
Maciej Dobrzynski
Browse files
Bug fixes
parent
602f8b92
Changes
3
Hide whitespace changes
Inline
Side-by-side
modules/auxfunc.R
View file @
a8f6e87c
...
...
@@ -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_W
ell
=
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_RealT
ime
=
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
(
w
ell
=
rep
(
LETTERS
[
1
:
in.nwells
],
each
=
in.ntpts
*
in.nfov
*
in.ntracks
/
in.nwells
),
group
=
rep
(
1
:
in.nfov
,
each
=
in.ntpts
*
in.ntracks
),
t
ime
=
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
)
}
...
...
server.R
View file @
a8f6e87c
...
...
@@ -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|M
eas'
,
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|M
eas'
,
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'
,
...
...
ui.R
View file @
a8f6e87c
...
...
@@ -64,7 +64,7 @@ shinyUI(fluidPage(
uiOutput
(
'varSelTime'
),
uiOutput
(
'varSelMeas1'
),
radioButtons
(
'inSelMath'
,
width
=
'
2
5%'
,
'inSelMath'
,
width
=
'5
0
%'
,
'Math on 1st and 2nd meas.:'
,
c
(
'None'
=
''
,
...
...
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