Skip to content

GitLab

In order to mitigate against the brute force attacks against Gitlab accounts, we are moving to all edu-ID Logins. We would like to remind you to link your account with your edu-id. Login will be possible only by edu-ID after November 30, 2021. Here you can find the instructions for linking your account.

If you don't have a SWITCH edu-ID, you can create one with this guide here

kind regards

This Server has been upgraded to GitLab release 14.2.6

Commit 5f86a0fd authored by Maciej Dobrzynski's avatar Maciej Dobrzynski
Browse files

Bug fixes in UI

parent ffab21c1
Hide whitespace changes
Inline Side-by-side
Showing with 58 additions and 57 deletions
modules/auxfunc.R
View file @ 5f86a0fd
......@@ -25,15 +25,22 @@ DEB = T
# PLOTFONTFACETSTRIP = 10
# PLOTFONTLEGEND = 8
PLOTFONTBASE = 12
PLOTFONTAXISTEXT = 12
PLOTFONTAXISTITLE = 12
PLOTFONTFACETSTRIP = 16
PLOTFONTLEGEND = 12
PLOTFONTBASE = 16
PLOTFONTAXISTEXT = 16
PLOTFONTAXISTITLE = 16
PLOTFONTFACETSTRIP = 20
PLOTFONTLEGEND = 16
# height (in pixels) of ribbon and single traj. plots
PLOTRIBBONHEIGHT = 500 # in pixels
PLOTTRAJHEIGHT = 500 # in pixels
PLOTPSDHEIGHT = 500 # in pixels
PLOTBOXHEIGHT = 500 # in pixels
PLOTSCATTERHEIGHT = 500 # in pixels
PLOTWIDTH = 85 # in percent
# default number of facets in plots
PLOTNFACETDEFAULT = 2
PLOTNFACETDEFAULT = 3
# internal column names
COLRT = 'realtime'
......@@ -499,7 +506,7 @@ LOCrotatedAxisElementText = function(angle, position='x', size = 12){
rads = (-angle - positions[[ position ]])*pi/180
hjust = round((1 - sin(rads)))/2
vjust = round((1 + cos(rads)))/2
element_text(size = 12, angle = angle, vjust = vjust, hjust = hjust)
element_text(size = size, angle = angle, vjust = vjust, hjust = hjust)
}
# Plot individual time series
......
modules/boxPlot.R
View file @ 5f86a0fd
......@@ -43,7 +43,7 @@ modBoxPlotUI = function(id, label = "Plot Box-plots") {
numericInput(
ns('inPlotBoxWidth'),
'Width [%]:',
value = 100,
value = PLOTWIDTH,
min = 10,
width = '100px',
step = 10
......@@ -51,7 +51,7 @@ modBoxPlotUI = function(id, label = "Plot Box-plots") {
numericInput(
ns('inPlotBoxHeight'),
'Height [px]:',
value = 800,
value = PLOTBOXHEIGHT,
min = 100,
width = '100px',
step = 50
......
modules/clDistPlot.R
View file @ 5f86a0fd
......@@ -7,7 +7,7 @@ modClDistPlotUI = function(id, label = "Plot Fractions WIthin Clusters") {
"45 deg" = 45,
"90 deg" = 90)),
actionButton(ns('butPlotClDist'), 'Plot!'),
plotOutput(ns('outPlotClDist'), height = '800px', width = 'auto'),
plotOutput(ns('outPlotClDist'), height = PLOTBOXHEIGHT, width = 'auto'),
downPlotUI(ns('downPlotClDist'), "Download PDF")
)
}
......@@ -63,7 +63,7 @@ modClDistPlot = function(input, output, session, in.data, in.cols = NULL, in.fna
in.font.strip = PLOTFONTFACETSTRIP,
in.font.legend = PLOTFONTLEGEND) +
theme(
axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate))
axis.text.x = LOCrotatedAxisElementText(as.numeric(input$rBAxisLabelsRotate), size = PLOTFONTAXISTEXT)
)
return(p.out)
......
modules/clHeatmapPlot.R deleted 100644 → 0
View file @ ffab21c1
modHeatmapPlotUI = function(id, label = "Plot Heatmap") {
ns <- NS(id)
}
modHeatmapPlot = function(input, output, session, in.data) {
ns <- session$ns
}
\ No newline at end of file
modules/selOutliers.R
View file @ 5f86a0fd
......@@ -67,7 +67,7 @@ modSelOutliers = function(input, output, session, in.data) {
output$txtOutliersPerc <- renderText({
cat(file = stdout(), 'modSelOutliers: txtOutliersPerc\n')
sprintf('<b>%d total track(s)<br>%d outlier track(s)<br>%d outlier point(s)</b><br>',
sprintf('<b>%d total track(s)<br>%d removed track(s)<br>%d removed point(s)</b><br>',
nCellsCounter[['nCellsOrig']],
nCellsCounter[['nCellsOrig']] - nCellsCounter[['nCellsAfter']],
nCellsCounter[['nOutlierTpts']])
......
modules/tabScatter.R
View file @ 5f86a0fd
......@@ -41,7 +41,7 @@ tabScatterPlotUI <- function(id, label = "Comparing t-points") {
numericInput(
ns('inPlotHeight'),
'Display plot height [px]',
value = 1000,
value = PLOTSCATTERHEIGHT,
min = 100,
step = 100
),
......
modules/trajPlot.R
View file @ 5f86a0fd
......@@ -16,7 +16,7 @@ modTrajPlotUI = function(id, label = "Plot Individual Time Series") {
tagList(
fluidRow(
column(
3,
2,
numericInput(
ns('inPlotTrajFacetNcol'),
'#Columns:',
......@@ -29,7 +29,7 @@ modTrajPlotUI = function(id, label = "Plot Individual Time Series") {
actionButton(ns('butPlotTraj'), 'Plot!')
),
column(
3,
2,
checkboxGroupInput(ns('chBPlotTrajStat'), 'Stats:', list('Mean' = 'mean', '95% conf. interv.' = 'CI', 'Std. error' = 'SE'))
),
column(
......@@ -48,20 +48,19 @@ modTrajPlotUI = function(id, label = "Plot Individual Time Series") {
),
column(
3,
2,
numericInput(
ns('inPlotTrajWidth'),
'Width [%]:',
value = 100,
value = PLOTWIDTH,
min = 10,
max = 100,
width = '100px',
step = 10
),
numericInput(
ns('inPlotTrajHeight'),
'Height [px]:',
value = 800,
value = PLOTTRAJHEIGHT,
min = 100,
width = '100px',
step = 50
......
modules/trajPsdPlot.R
View file @ 5f86a0fd
......@@ -8,36 +8,43 @@ modPSDPlotUI = function(id, label = "Plot PSD of average trajectory.") {
tagList(
fluidRow(
column(
3,
2,
radioButtons(ns('rBPSDmethod'), 'Method for PSD estimation:', list('Smoothed Fourier' = 'pgram', 'AR Fit' = 'ar')),
checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
actionButton(ns('butPlotTraj'), 'Plot!')
),
column(
3,
2,
selectInput(ns('inPSDxchoice'), 'X-axis:', list('Period'= TRUE, 'Frequency'= FALSE)),
numericInput(ns('ninPSDsamplFreq'), '# time units between 2 points:', value = 1, min = 0, step = 1)
),
column(
3,
selectInput(ns('inPSDlogtype'), 'Transformation:', list('1/x'='inverse_trans', 'log2'= 'log2', 'log10'= 'log10', 'ln'= 'log')),
checkboxGroupInput(ns('chBGPSDlogaxis'), 'Transform the axis:', list('x' = 'x', 'y' = 'y'), inline = TRUE)
2,
selectInput(ns('inPSDtransXtype'), 'Transform X-axis:', list('none' = 'none',
'1/x'='inverse_trans',
'log2'= 'log2',
'log10'= 'log10',
'ln'= 'log')),
selectInput(ns('inPSDtransYtype'), 'Transform Y-axis:', list('none' = 'none',
'1/y'='inverse_trans',
'log2'= 'log2',
'log10'= 'log10',
'ln'= 'log'))
),
column(
3,
2,
numericInput(
ns('inPlotTrajWidth'),
'Width [%]:',
value = 100,
min = 10,
max = 100,
width = '100px',
step = 10
),
numericInput(
ns('inPlotTrajHeight'),
'Height [px]:',
value = 800,
value = PLOTPSDHEIGHT,
min = 100,
width = '100px',
step = 50
......@@ -205,24 +212,24 @@ modPSDPlot = function(input, output, session,
in.font.axis.title = PLOTFONTAXISTITLE,
in.font.strip = PLOTFONTFACETSTRIP,
in.font.legend = PLOTFONTLEGEND)
# TODO: Restore tick labels when using inverse transformation
# See: https://stackoverflow.com/questions/56130614/ggplot2-missing-labels-after-custom-scaling-of-axis
inverse_trans <- scales::trans_new("myinverse", transform = function(x) 1/x,
inverse = function(x) 1/(1/x))
if("x" %in% input$chBGPSDlogaxis){
if(input$inPSDlogtype == "inverse_trans"){
p.out <- p.out + scale_x_continuous(trans = inverse_trans)
} else {
p.out <- p.out + scale_x_continuous(trans = input$inPSDlogtype)
}
if(input$inPSDtransXtype == "inverse_trans"){
p.out <- p.out + scale_x_continuous(trans = inverse_trans)
} else if (!(input$inPSDtransXtype == "none")) {
p.out <- p.out + scale_x_continuous(trans = input$inPSDtransXtype)
}
if("y" %in% input$chBGPSDlogaxis){
if(input$inPSDlogtype == "inverse_trans"){
p.out <- p.out + scale_y_continuous(trans = inverse_trans)
} else {
p.out <- p.out + scale_y_continuous(trans = input$inPSDlogtype)
}
if(input$inPSDtransYtype == "inverse_trans"){
p.out <- p.out + scale_y_continuous(trans = inverse_trans)
} else if (!(input$inPSDtransYtype == "none")) {
p.out <- p.out + scale_y_continuous(trans = input$inPSDtransYtype)
}
return(p.out)
}
}
\ No newline at end of file
modules/trajRibbonPlot.R
View file @ 5f86a0fd
......@@ -6,7 +6,7 @@ modTrajRibbonPlotUI = function(id, label = "Plot Individual Time Series") {
tagList(
fluidRow(
column(
3,
2,
checkboxInput(ns('chBplotTrajInt'), 'Interactive Plot'),
radioButtons(ns('rBlegendPos'), 'Legend placement:', list('top' = 'top', 'right' = 'right')),
actionButton(ns('butPlotTraj'), 'Plot!')
......@@ -16,20 +16,19 @@ modTrajRibbonPlotUI = function(id, label = "Plot Individual Time Series") {
sliderInput(ns('sliPlotTrajSkip'), 'Plot every n-th point:', min = 1, max = 10, value = 1, step = 1)
),
column(
3,
2,
numericInput(
ns('inPlotTrajWidth'),
'Width [%]:',
value = 100,
value = PLOTWIDTH,
min = 10,
max = 100,
width = '100px',
step = 10
),
numericInput(
ns('inPlotTrajHeight'),
'Height [px]:',
value = 800,
value = PLOTRIBBONHEIGHT,
min = 100,
width = '100px',
step = 50
......
ui.R
View file @ 5f86a0fd
......@@ -18,7 +18,7 @@ shinyUI(fluidPage(
title = "Timecourse Inspector",
sidebarLayout(
sidebarPanel(
sidebarPanel(width = 3,
#Selector for file upload
fileInput(
'inFileLoadNuc',
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment