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server.R
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library("irr")
library("sjPlot")
library("plotly")
library("shiny")
library("shinydashboard")
source("allStats.R")
# Define server logic required to build shiny app
function(input, output) {
###MENU HOME###
output$overviewTxt1 <- renderUI({
a(HTML("<font size=6>About the Challenge</font></b>"), href=paste("https://blog.ismrm.org/2019/12/12/reproducibility-challenge-2020-join-the-reproducible-research-and-quantitative-mr-study-groups-in-their-efforts-to-standardize-t1-mapping/"), target="_blank")
})
output$overviewTxt2 <- renderUI({
a(HTML("<font size=6>GitHub Organization</font></b>"), href=paste("https://github.com/rrsg2020/"), target="_blank")
})
output$overviewTxt3 <- renderUI({
a(HTML("<font size=6>Dataset OSF</font></b>"), href=paste("https://osf.io/ywc9g/"), target="_blank")
})
output$overviewTxt4 <- renderUI({
a(HTML("<font size=6>General Dashboard</font></b>"), href=paste("http://rrsg2020.herokuapp.com/"), target="_blank")
})
###MAGNITUDE VS COMPLEX ANALYSIS###
MagCom_colors <- setNames(viridis(length(cases)), unique(magVScomp$dataMagComp$sid))
output$MagComp <- renderPlotly({
if (input$typeComparison == "Difference"){
plot_ly(magVScomp$dataMagComp, x = ~refT1, y = ~abs(diff), split = ~as.factor(sid), color = ~as.factor(sid), colors = MagCom_colors) %>%
filter(sid %in% input$DiffSitesID) %>%
add_trace(type = 'scatter', mode = 'lines+markers',
hoverinfo = 'text',
text = ~paste('<br> Site: ', sid,
'<br> Difference (ms): ', signif(abs(diff),3),
'<br> Reference T1 (ms): ', signif(refT1,5))) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Difference (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(abs(magVScomp$dataMagComp),2,max))[4]+5)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.8, y=0.95, bgcolor = "rgba(0,0,0,0)"))
}
else if (input$typeComparison == "Difference (%)"){
plot_ly(magVScomp$dataMagComp, x = ~refT1, y = ~abs(percDiff), split = ~as.factor(sid), color = ~as.factor(sid), colors = MagCom_colors) %>%
filter(sid %in% input$DiffSitesID) %>%
add_trace(type = 'scatter', mode = 'lines+markers',
hoverinfo = 'text',
text = ~paste('<br> Site: ', sid,
'<br> Difference (%): ', signif(abs(percDiff),4),
'<br> Reference T1 (ms): ', signif(refT1,5))) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Percentage difference (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(abs(magVScomp$dataMagComp),2,max))[5]+5)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.8, y=0.95, bgcolor = "rgba(0,0,0,0)"))
}
})
output$BAMagComp <- renderPlotly({
if (input$typeComparison == "Difference (%)"){
plot_ly(magVScomp$dataMagComp) %>%
add_trace(magVScomp$dataMagComp, x = ~average, y = ~percDiff, color = ~as.factor(sid),
colors = MagCom_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Difference (%): ', signif(percDiff,4),
'<br> Average T1 (ms): ', signif(average,5),
'<BR> Reference T1 (ms): ', signif(refT1,5),
'<br> ID: ', sid)) %>%
layout(xaxis = list(title=list(text="Average T1 (ms)", font=list(size=18)), tickfont=list(size=15), zeroline=F,
showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600)),
yaxis = list(title=list(text="Percentage difference (%)", font=list(size=18)), tickfont=list(size=15), zeroline=F,
showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(unname(apply(magVScomp$dataMagComp,2,min))[5]-20,unname(apply(magVScomp$dataMagComp,2,max))[5]+20)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.85, y=0.95, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600), y = mean(magVScomp$dataMagComp$percDiff),
type='scatter', mode = "lines", line = list(dash = "solid", width = 2, color = "black"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600),
y = mean(magVScomp$dataMagComp$percDiff) + 1.96*sd(magVScomp$dataMagComp$percDiff),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600),
y = mean(magVScomp$dataMagComp$percDiff) - 1.96*sd(magVScomp$dataMagComp$percDiff),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
layout(annotations = list(x=1400, y=mean(magVScomp$dataMagComp$percDiff)-10,
text=paste("Mean = ",signif(mean(magVScomp$dataMagComp$percDiff),3)),
showarrow = FALSE, font = list(size=12, color="black"))) %>%
layout(annotations = list(x=1400, y=mean(magVScomp$dataMagComp$percDiff) + 1.96*sd(magVScomp$dataMagComp$percDiff) + 10,
text=paste("Mean+1.96SD = ",signif(mean(magVScomp$dataMagComp$percDiff)+1.96*sd(magVScomp$dataMagComp$percDiff),3)),
showarrow = FALSE, font = list(size=12, color="firebrick"))) %>%
layout(annotations = list(x=1400, y=mean(magVScomp$dataMagComp$percDiff) - 1.96*sd(magVScomp$dataMagComp$percDiff) - 10,
text=paste("Mean-1.96SD = ",signif(mean(magVScomp$dataMagComp$percDiff)-1.96*sd(magVScomp$dataMagComp$percDiff),3)),
showarrow = FALSE, font = list(size=12, color="firebrick")))
}
else if (input$typeComparison == "Difference"){
plot_ly(magVScomp$dataMagComp) %>%
add_trace(magVScomp$dataMagComp, x = ~average, y = ~diff, color = ~as.factor(sid),
colors = MagCom_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Difference (ms): ', signif(diff,4),
'<br> Average T1 (ms): ', signif(average,5),
'<BR> Reference T1 (ms): ', signif(refT1,5),
'<br> ID: ', sid)) %>%
layout(xaxis = list(title=list(text="Average T1 (ms)", font=list(size=18)), tickfont=list(size=15), zeroline=F,
showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600)),
yaxis = list(title=list(text="Difference (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(unname(apply(magVScomp$dataMagComp,2,min))[4]-20,unname(apply(magVScomp$dataMagComp,2,max))[4]+20)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.85, y=0.95, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600), y = mean(magVScomp$dataMagComp$diff),
type='scatter', mode = "lines", line = list(dash = "solid", width = 2, color = "black"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600),
y = mean(magVScomp$dataMagComp$diff) + 1.96*sd(magVScomp$dataMagComp$diff),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,unname(apply(magVScomp$dataMagComp,2,max))[8]+600),
y = mean(magVScomp$dataMagComp$diff) - 1.96*sd(magVScomp$dataMagComp$diff),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
layout(annotations = list(x=1400, y=mean(magVScomp$dataMagComp$diff)-10,
text=paste("Mean = ",signif(mean(magVScomp$dataMagComp$diff),3)),
showarrow = FALSE, font = list(size=12, color="black"))) %>%
layout(annotations = list(x=1400, y=mean(magVScomp$dataMagComp$diff) + 1.96*sd(magVScomp$dataMagComp$diff) + 10,
text=paste("Mean+1.96SD = ",signif(mean(magVScomp$dataMagComp$diff)+1.96*sd(magVScomp$dataMagComp$diff),3)),
showarrow = FALSE, font = list(size=12, color="firebrick"))) %>%
layout(annotations = list(x=1400, y=mean(magVScomp$dataMagComp$diff) - 1.96*sd(magVScomp$dataMagComp$diff) - 10,
text=paste("Mean-1.96SD = ",signif(mean(magVScomp$dataMagComp$diff)-1.96*sd(magVScomp$dataMagComp$diff),3)),
showarrow = FALSE, font = list(size=12, color="firebrick")))
}
})
sphere_colors <- setNames(viridis(14), unique(signif(magVScomp$dataCorr$refT1,5)))
output$CorrMagComp <- renderPlotly({
plotly_plot <- plot_ly(magVScomp$dataCorr) %>%
filter(sid %in% input$CorrSitesID) %>%
add_trace(magVScomp$dataCorr, x = ~Complex, y = ~Magnitude, color = ~as.factor(signif(refT1,5)),
colors = sphere_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Complex (ms): ', signif(Complex,5),
'<br> Magnitude (ms): ', signif(Magnitude,5),
'<br> Reference T1 (ms): ', signif(refT1,5),
'<br> ID: ', sid)) %>%
layout(xaxis = list(title=list(text="Complex T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$dataCorr,2,max))[5]+100)),
yaxis = list(title=list(text="Magnitude T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$dataCorr,2,max))[4]+100)),
legend = list(title=list(text="<b>T1 (ms)</b>", font=list(size = 10)),
font = list(size = 9), yanchor="top", xanchor="left", x=0.01, y=0.99, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0, unname(apply(magVScomp$dataCorr,2,max))[5]+100), y = c(0, unname(apply(magVScomp$dataCorr,2,max))[4]+100),
type = "scatter", mode = "lines", line = list(color = 'black', width = 2), showlegend = FALSE)
})
output$PearsonCorr <- renderTable(magVScomp$PearsonCorr)
output$DispAllPointsMagComp_oneSite <- renderPlotly({
plot_ly(magVScomp$PearsonCorrSphere) %>%
filter(sid_long %in% input$CorrSitesIDallDP) %>%
add_trace(magVScomp$PearsonCorrSphere, x = ~compData, y = ~magData, color = ~as.factor(signif(refT1_long,5)),
colors = sphere_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Complex (ms): ', signif(compData,5),
'<br> Magnitude (ms): ', signif(magData,5),
'<br> Reference T1 (ms): ', signif(refT1_long,5),
'<br> ID: ', sid_long)) %>%
layout(xaxis = list(title=list(text="Complex T1 value (ms)", font=list(size=18)), tickfont=list(size=15), zeroline=F,
showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$PearsonCorrSphere,2,max))[5]+100)),
yaxis = list(title=list(text="Magnitude T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$PearsonCorrSphere,2,max))[4]+100)),
legend = list(title=list(text="<b>T1 (ms)</b>", font=list(size = 10)),
font = list(size = 9), yanchor="top", xanchor="left", x=0.01, y=0.99, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0, unname(apply(magVScomp$PearsonCorrSphere,2,max))[5]+100), y = c(0, unname(apply(magVScomp$PearsonCorrSphere,2,max))[4]+100),
type = "scatter", mode = "lines", line = list(color = 'black', width = 2), showlegend = FALSE)
})
toListen <- reactive({input$CorrSitesIDallDP})
observeEvent(toListen(), {
dataMagCompSphere = comparison_magnitude_complex(cases)
spheres = 1:14
refT1 = temperature_correction(20,42)
corr_per_sphere = reactiveValues(df = data.frame(Sphere=as.integer(), ReferenceT1=as.numeric(), Pearson=as.numeric(), Lin=as.numeric()))
for (ii in seq(1,length(spheres))){
data_per_sphere = subset(dataMagCompSphere$PearsonCorrSphere, sid_long == input$CorrSitesIDallDP & sph_long == spheres[ii])
corr_per_sphere$df[ii,1] = spheres[ii]
corr_per_sphere$df[ii,2] = signif(refT1[ii],5)
corr_per_sphere$df[ii,3] = cor(data_per_sphere$magData,data_per_sphere$compData)
corr_per_sphere$df[ii,4] = CCC(data_per_sphere$magData,data_per_sphere$compData)[[1]][1]
}
output$PearsonAllPointsMagComp_oneSite <- renderTable({corr_per_sphere$df})
})
output$DispAllPointsMagComp_allSites <- renderPlotly({
plot_ly(magVScomp$PearsonCorrSphere) %>%
add_trace(magVScomp$PearsonCorrSphere, x = ~compData, y = ~magData, color = ~as.factor(signif(refT1_long,5)),
colors = sphere_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Complex (ms): ', signif(compData,5),
'<br> Magnitude (ms): ', signif(magData,5),
'<br> Reference T1 (ms): ', signif(refT1_long,5),
'<br> ID: ', sid_long)) %>%
layout(xaxis = list(title=list(text="Complex T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$PearsonCorrSphere,2,max))[5]+100)),
yaxis = list(title=list(text="Magnitude T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,unname(apply(magVScomp$PearsonCorrSphere,2,max))[4]+100)),
legend = list(title=list(text="<b>T1 (ms)</b>", font=list(size = 10)),
font = list(size = 9), yanchor="bottom", xanchor="right", x=0.99, y=0.01, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0, unname(apply(magVScomp$PearsonCorrSphere,2,max))[5]+100), y = c(0, unname(apply(magVScomp$PearsonCorrSphere,2,max))[4]+100),
type = "scatter", mode = "lines", line = list(color = 'black', width = 2), showlegend = FALSE)
})
spheres = 1:14
refT1 = temperature_correction(20,42)
corr_per_sphere = data.frame(Sphere=as.integer(), ReferenceT1=as.numeric(), Pearson=as.numeric(), Lin=as.numeric())
for (ii in seq(1,length(spheres))){
data_per_sphere = subset(magVScomp$PearsonCorrSphere, sph_long == spheres[ii])
corr_per_sphere[ii,1] = spheres[ii]
corr_per_sphere[ii,2] = signif(refT1[ii],5)
corr_per_sphere[ii,3] = cor(data_per_sphere$magData,data_per_sphere$compData)
corr_per_sphere[ii,4] = CCC(data_per_sphere$magData,data_per_sphere$compData)[[1]][1]
}
output$PearsonAllPointsMagComp_allSites <- renderTable({corr_per_sphere})
###NIST PHANTOM (MEASURED VS REFRENCE T1 ANALYSIS)###
sitesFiltered_colors <- setNames(viridis(length(filteredSites)), unique(MeasSites$dataSite$ID_Site))
output$CompFiltSites <- renderPlotly({
plot_ly(MeasSites$dataSite, x = ~refT1, y = ~Mean, split = ~ID_Site, color = ~ID_Site, colors = sitesFiltered_colors,
error_y = ~list(array = Std, color = '#000000')) %>%
filter(sid %in% input$FiltSitesID) %>%
add_trace(type = 'scatter', mode = 'lines+markers',
hoverinfo = 'text',
text = ~paste('<br> Site: ', sid,
'<br> Measured T1: ', signif(Mean,6),
'<br> Reference T1: ', signif(refT1,6),
'<br> Sphere: ', Sphere)) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)",font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(MeasSites$dataSite,2,max))[4])+100)),
yaxis = list(title=list(text="Mean T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(MeasSites$dataSite,2,max))[5])+100)),
legend = list(title=list(text="<b>Site ID</b>", font=list(size = 10)),
font = list(size = 9), xanchor="left", yanchor="top", x=0.01, y=0.8, bgcolor = "rgba(0,0,0,0)"))
})
output$sdFilteredSites <- renderPlotly({
sdFiltered_colors <- setNames(viridis(length(filteredSites)), unique(sdFilteredSites$stdData$ID_Site))
plot_ly(sdFilteredSites$stdData, x = ~reference, y = ~stdValues/reference, split = ~ID_Site, color = ~ID_Site, colors = sdFiltered_colors) %>%
filter(sid %in% input$FiltSitesID) %>%
add_trace(type = 'scatter', mode = 'lines+markers',
hoverinfo = 'text',
text = ~paste('<br> SD/Reference T1: ', signif(stdValues/reference,3),
'<br> SD: ', signif(stdValues,3),
'<br> Reference T1: ', signif(reference,5),
'<br> Site: ', ID_Site)) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="SD/Reference T1", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,0.2)),
legend = list(title=list(text="<b>Site ID</b>", font=list(size = 10)),
font = list(size = 9), xanchor="right", yanchor="top", x=0.99, y=0.8, bgcolor = "rgba(0,0,0,0)"))
})
output$DispAllPoints <- renderPlotly({
if (input$DispAllSite == "Montreal"){
DispersionAllPoints = SiteMontreal
}
else if (input$DispAllSite == "Germany"){
DispersionAllPoints = SiteGermany
}
else if (input$DispAllSite == "US"){
DispersionAllPoints = SiteUS
}
else if (input$DispAllSite == "London"){
DispersionAllPoints = SiteLondon
}
else if (input$DispAllSite == "Australia"){
DispersionAllPoints = SiteAustralia
}
specSite_colors <- setNames(viridis(length(unique(DispersionAllPoints$dataSite_long$ID_Site_long))), unique(DispersionAllPoints$dataSite_long$ID_Site_long))
plot_ly(DispersionAllPoints$dataSite_long) %>%
add_trace(DispersionAllPoints$dataSite_long, x = ~t1_long, y = ~siteData, color = ~ID_Site_long,
colors = specSite_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Measured T1 value (ms): ', signif(siteData,5),
'<br> Reference T1 value (ms): ', signif(t1_long,5),
'<br> ID: ', sid_long)) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(DispersionAllPoints$dataSite_long,2,max))[4])+100)),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(DispersionAllPoints$dataSite_long,2,max))[5])+100)),
legend = list(title=list(text="<b>Site ID</b>", font=list(size = 10)),
font = list(size = 9), x=0.75, y=0.01, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0, as.numeric(unname(apply(DispersionAllPoints$dataSite_long,2,max))[4])+100),
y = c(0, as.numeric(unname(apply(DispersionAllPoints$dataSite_long,2,max))[5])+100),
type = "scatter", mode = "lines", line = list(color = 'black', width = 2), showlegend = FALSE)
})
output$Disp4Site <- renderPlotly({
if (input$selectCompSite == "Montreal"){
RefVSMeas = measuredT1_against_referenceT1(scans = Montreal)
}
else if (input$selectCompSite == "Germany"){
RefVSMeas = measuredT1_against_referenceT1(scans = Germany)
}
else if (input$selectCompSite == "US"){
RefVSMeas = measuredT1_against_referenceT1(scans = US)
}
else if (input$selectCompSite == "London"){
RefVSMeas = measuredT1_against_referenceT1(scans = London)
}
else if (input$selectCompSite == "Australia"){
RefVSMeas = measuredT1_against_referenceT1(scans = Australia)
}
sitesFiltBA_colors <- setNames(viridis(length(unique(RefVSMeas$BAData$ID_Site))), unique(RefVSMeas$BAData$ID_Site))
plot_ly(RefVSMeas$BAData) %>%
add_trace(RefVSMeas$BAData, x = ~reference, y = ~measValue, color = ~ID_Site,
colors = sitesFiltBA_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Measured T1 value (ms): ', signif(measValue,5),
'<br> Reference T1 value (ms): ', signif(reference,5),
'<br> Sphere: ', sph)) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[6])+100)),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[5])+100)),
legend = list(title=list(text="<b>Site ID</b>", font=list(size = 10)),
font = list(size = 9), x=0.75, y=0.01, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[6])+100), y = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[5])+100),
type = "scatter", mode = "lines", line = list(color = 'black', width = 2), showlegend = FALSE)
})
output$BA4Site <- renderPlotly({
if (input$selectCompSite == "Montreal"){
RefVSMeas = measuredT1_against_referenceT1(scans = Montreal)
}
else if (input$selectCompSite == "Germany"){
RefVSMeas = measuredT1_against_referenceT1(scans = Germany)
}
else if (input$selectCompSite == "US"){
RefVSMeas = measuredT1_against_referenceT1(scans = US)
}
else if (input$selectCompSite == "London"){
RefVSMeas = measuredT1_against_referenceT1(scans = London)
}
else if (input$selectCompSite == "Australia"){
RefVSMeas = measuredT1_against_referenceT1(scans = Australia)
}
sitesFiltBA_colors <- setNames(viridis(length(unique(RefVSMeas$BAData$ID_Site))), unique(RefVSMeas$BAData$ID_Site))
plot_ly(RefVSMeas$BAData) %>%
add_trace(RefVSMeas$BAData, x = ~average, y = ~perc_difference, color = ~ID_Site,
colors = sitesFiltBA_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Difference (%): ', signif(perc_difference,4),
'<br> Average T1: ', signif(average,5),
'<BR> Reference T1: ', signif(reference,5),
'<br> Sphere: ', sph)) %>%
layout(xaxis = list(title=list(text="Average T1 (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800)),
yaxis = list(title=list(text="Percentage difference (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(-40,40)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.75, y=0.95, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800), y = mean(RefVSMeas$BAData$perc_difference),
type='scatter', mode = "lines", line = list(dash = "solid", width = 2, color = "black"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800),
y = mean(RefVSMeas$BAData$perc_difference) + 1.96*sd(RefVSMeas$BAData$perc_difference),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800),
y = mean(RefVSMeas$BAData$perc_difference) - 1.96*sd(RefVSMeas$BAData$perc_difference),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
layout(annotations = list(x=1500, y=mean(RefVSMeas$BAData$perc_difference)-3,
text=paste("Mean = ",signif(mean(RefVSMeas$BAData$perc_difference),3)),
showarrow = FALSE, font = list(size=12, color="black"))) %>%
layout(annotations = list(x=1500, y=mean(RefVSMeas$BAData$perc_difference) + 1.96*sd(RefVSMeas$BAData$perc_difference) + 5,
text=paste("Mean+1.96SD = ",signif(mean(RefVSMeas$BAData$perc_difference)+1.96*sd(RefVSMeas$BAData$perc_difference),3)),
showarrow = FALSE, font = list(size=12, color="firebrick"))) %>%
layout(annotations = list(x=1500, y=mean(RefVSMeas$BAData$perc_difference) - 1.96*sd(RefVSMeas$BAData$perc_difference) - 5,
text=paste("Mean-1.96SD = ",signif(mean(RefVSMeas$BAData$perc_difference)-1.96*sd(RefVSMeas$BAData$perc_difference),3)),
showarrow = FALSE, font = list(size=12, color="firebrick")))
})
output$Disp4Vendor <- renderPlotly({
if (input$selectCompVendor == "Siemens"){
RefVSMeas = measuredT1_against_referenceT1(scans = Siemens)
}
else if (input$selectCompVendor == "GE"){
RefVSMeas = measuredT1_against_referenceT1(scans = GE)
}
else if (input$selectCompVendor == "Philips"){
RefVSMeas = measuredT1_against_referenceT1(scans = Philips)
}
vendorFiltBA_colors <- setNames(viridis(length(unique(RefVSMeas$BAData$ID_Vendor))), unique(RefVSMeas$BAData$ID_Vendor))
plot_ly(RefVSMeas$BAData) %>%
add_trace(RefVSMeas$BAData, x = ~reference, y = ~measValue, color = ~ID_Vendor,
colors = vendorFiltBA_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Measured T1 value (ms): ', signif(measValue,5),
'<br> Reference T1 value (ms): ', signif(reference,5),
'<br> Sphere: ', sph)) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[6])+100)),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[5])+100)),
legend = list(title=list(text="<b>MRI vendor</b>", font=list(size = 10)),
font = list(size = 9), x=0.67, y=0.01, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[6])+100), y = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[5])+100),
type = "scatter", mode = "lines", line = list(color = 'black', width = 2), showlegend = FALSE)
})
output$BA4Vendor <- renderPlotly({
if (input$selectCompVendor == "Siemens"){
RefVSMeas = measuredT1_against_referenceT1(scans = Siemens)
}
else if (input$selectCompVendor == "GE"){
RefVSMeas = measuredT1_against_referenceT1(scans = GE)
}
else if (input$selectCompVendor == "Philips"){
RefVSMeas = measuredT1_against_referenceT1(scans = Philips)
}
vendorFiltBA_colors <- setNames(viridis(length(unique(RefVSMeas$BAData$ID_Vendor))), unique(RefVSMeas$BAData$ID_Vendor))
plot_ly(RefVSMeas$BAData) %>%
add_trace(RefVSMeas$BAData, x = ~average, y = ~perc_difference, color = ~ID_Vendor,
colors = vendorFiltBA_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Difference (%): ', signif(perc_difference,4),
'<br> Average T1: ', signif(average,5),
'<BR> Reference T1: ', signif(reference,5),
'<br> Sphere: ', sph)) %>%
layout(xaxis = list(title=list(text="Average T1 (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800)),
yaxis = list(title=list(text="Percentage difference (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(-40,40)),
legend = list(title=list(text="<b>MRI vendor</b>"), x=0.72, y=0.95, bgcolor = "rgba(0,0,0,0)")) %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800), y = mean(RefVSMeas$BAData$perc_difference),
type='scatter', mode = "lines", line = list(dash = "solid", width = 2, color = "black"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800),
y = mean(RefVSMeas$BAData$perc_difference) + 1.96*sd(RefVSMeas$BAData$perc_difference),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
add_trace(x = c(0,as.numeric(unname(apply(RefVSMeas$BAData,2,max))[9])+800),
y = mean(RefVSMeas$BAData$perc_difference) - 1.96*sd(RefVSMeas$BAData$perc_difference),
type='scatter', mode = "lines", line = list(dash = "dash", color = "firebrick"),
showlegend = FALSE, hoverinfo = "none") %>%
layout(annotations = list(x=1500, y=mean(RefVSMeas$BAData$perc_difference)-3,
text=paste("Mean = ",signif(mean(RefVSMeas$BAData$perc_difference),3)),
showarrow = FALSE, font = list(size=12, color="black"))) %>%
layout(annotations = list(x=1500, y=mean(RefVSMeas$BAData$perc_difference) + 1.96*sd(RefVSMeas$BAData$perc_difference) + 5,
text=paste("Mean+1.96SD = ",signif(mean(RefVSMeas$BAData$perc_difference)+1.96*sd(RefVSMeas$BAData$perc_difference),3)),
showarrow = FALSE, font = list(size=12, color="firebrick"))) %>%
layout(annotations = list(x=1500, y=mean(RefVSMeas$BAData$perc_difference) - 1.96*sd(RefVSMeas$BAData$perc_difference) - 5,
text=paste("Mean-1.96SD = ",signif(mean(RefVSMeas$BAData$perc_difference)-1.96*sd(RefVSMeas$BAData$perc_difference),3)),
showarrow = FALSE, font = list(size=12, color="firebrick")))
})
output$AcErrorAllPoints <- renderPlotly({
if (input$AcErrorAllSite == "Montreal"){
AcErrorAllPoints = SiteMontreal
}
else if (input$AcErrorAllSite == "Germany"){
AcErrorAllPoints = SiteGermany
}
else if (input$AcErrorAllSite == "US"){
AcErrorAllPoints = SiteUS
}
else if (input$AcErrorAllSite == "London"){
AcErrorAllPoints = SiteLondon
}
else if (input$AcErrorAllSite == "Australia"){
AcErrorAllPoints = SiteAustralia
}
AcErrorAllPoints = subset(AcErrorAllPoints$dataSite_long, ac_error <= input$errorThr[2])
specSite_colors <- setNames(viridis(length(unique(AcErrorAllPoints$ID_Site_long))), unique(AcErrorAllPoints$ID_Site_long))
plot_ly(AcErrorAllPoints) %>%
add_trace(AcErrorAllPoints, x = ~t1_long, y = ~ac_error, color = ~ID_Site_long,
colors = specSite_colors, type = 'scatter', mode = 'markers', marker = list(size = 8),
hoverinfo = 'text',
text = ~paste('<br> Accuracy Error (%): ', signif(ac_error,5),
'<br> Reference T1 value (ms): ', signif(t1_long,5),
'<br> ID: ', sid_long)) %>%
layout(xaxis = list(title=list(text="Reference T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(AcErrorAllPoints,2,max))[4])+100)),
yaxis = list(title=list(text="Accuracy Error (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,60)),
legend = list(title=list(text="<b>Site ID</b>", font=list(size = 10)),
font = list(size = 9), x=0.75, y=0.99, bgcolor = "rgba(0,0,0,0)"))
})
output$HSF1 <- renderPlotly({HSFData$diffBootstrapDiff[[14]]})
output$HSF2 <- renderPlotly({HSFData$diffBootstrapDiff[[13]]})
output$HSF3 <- renderPlotly({HSFData$diffBootstrapDiff[[12]]})
output$HSF4 <- renderPlotly({HSFData$diffBootstrapDiff[[11]]})
output$HSF5 <- renderPlotly({HSFData$diffBootstrapDiff[[10]]})
output$HSF6 <- renderPlotly({HSFData$diffBootstrapDiff[[9]]})
output$HSF7 <- renderPlotly({HSFData$diffBootstrapDiff[[8]]})
output$HSF8 <- renderPlotly({HSFData$diffBootstrapDiff[[7]]})
output$HSF9 <- renderPlotly({HSFData$diffBootstrapDiff[[6]]})
output$HSF10 <- renderPlotly({HSFData$diffBootstrapDiff[[5]]})
output$HSF11 <- renderPlotly({HSFData$diffBootstrapDiff[[4]]})
output$HSF12 <- renderPlotly({HSFData$diffBootstrapDiff[[3]]})
output$HSF13 <- renderPlotly({HSFData$diffBootstrapDiff[[2]]})
output$HSF14 <- renderPlotly({HSFData$diffBootstrapDiff[[1]]})
###HUMAN DATASET ANALYSIS###
output$boxPlotHuman <- renderPlotly({
sitesHuman$dataLong_human$roi_long <- factor(sitesHuman$dataLong_human$roi_long,
c("Genu WM", "splenium WM", "Deep GM", "Cortical GM"))
plot_ly(sitesHuman$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanMEX_all <- renderPlotly({
plot_ly(sitesHuman_Mexico$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanCAN_all <- renderPlotly({
plot_ly(sitesHuman_Canada$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanUS_all <- renderPlotly({
sitesHuman_US$dataLong_human$roi_long <- factor(sitesHuman_US$dataLong_human$roi_long,
c("Genu WM", "splenium WM", "Deep GM", "Cortical GM"))
plot_ly(sitesHuman_US$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanITA_all <- renderPlotly({
plot_ly(sitesHuman_Italy$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanGER_all <- renderPlotly({
plot_ly(sitesHuman_Germany$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanAUS_all <- renderPlotly({
plot_ly(sitesHuman_Australia$dataLong_human, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), orientation="h", xanchor="center",
x=0.5, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
output$humanMEX_vendor <- renderPlotly({
if (input$selectMEXVendor == "Philips"){
dataMEX_vendor = subset(sitesHuman_Mexico$dataLong_human, as.character(vendor_long)=="Philips")
}
else if (input$selectMEXVendor == "GE"){
dataMEX_vendor = subset(sitesHuman_Mexico$dataLong_human, as.character(vendor_long)=="GE")
}
plot_ly(dataMEX_vendor, x = ~roi_long, y = ~siteData, color = ~roi_long,
type = 'violin', box = list(visible = TRUE), meanline = list(visible = TRUE)) %>%
add_trace(hoveron = 'points+violins', points = 'all', hoverinfo = 'text',
text = ~paste0('<br> Measured value: ', signif(siteData,5),
'<br>ROI: ', roi_long,
'<br>SID: ', factor(sid_long)), showlegend = FALSE) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(as.numeric(unname(apply(sitesHuman_Mexico$dataLong_human,2,min))[6])-100,
as.numeric(unname(apply(sitesHuman_Mexico$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), x=0.75, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
sitesHuman_colors <- setNames(rainbow(length(listHumanData)), unique(dfmeanHuman$Site))
output$CompHumanSites <- renderPlotly({
plot_ly(dfmeanHuman, x = ~roi_lab, y = ~dif, split = ~Site, color = ~Site, colors = sitesHuman_colors) %>%
filter(Site %in% input$FiltHumanSitesID) %>%
add_trace(type = 'scatter', mode = 'lines+markers',
hoverinfo = 'text',
text = ~paste('<br> Site: ', Site,
'<br> Difference (%): ', signif(dif,4),
'<br> ROI: ', roi_lab)) %>%
layout(xaxis = list(title=list(text="Region of Interest", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Percentage difference (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(-30,70)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.8, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
sitesHuman$dataLong_human$age_long=as.numeric(as.character(sitesHuman$dataLong_human$age_long))
output$humanAge_all <- renderPlotly({
#sdFiltered_colors <- setNames(rainbow(nrow(sdFilteredSites$stdData)), sdFilteredSites$stdData$ID_Site)
plot_ly(sitesHuman$dataLong_human[order(sitesHuman$dataLong_human$age_long),], x = ~age_long, y = ~siteData, split = ~roi_long) %>%
add_trace(type = 'scatter', mode = 'markers',
hoverinfo = 'text',
text = ~paste('<br> Site: ', sid_long,
'<br> ROI: ', roi_long,
'<br> T1 value: ', signif(siteData,5))) %>%
layout(xaxis = list(title=list(text="Age (years)", font=list(size=18)), categoryarray = ~names, categoryorder = "array", tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F),
yaxis = list(title=list(text="Measured T1 value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F,
range=list(0,as.numeric(unname(apply(sitesHuman$dataLong_human,2,max))[6])+100)),
legend = list(title=list(text="<b>ROI</b>"), x=0.75, y=0.95, bgcolor = "rgba(0,0,0,0)"))
})
#covs_colors <- setNames(rainbow(12), unique(compNISTHuman$Site))
maxX = as.numeric(unname(apply(compNISTHuman,2,max, na.rm=T))[4])
maxY = as.numeric(unname(apply(compNISTHuman,2,max, na.rm=T))[5])
maxSampleSize = as.numeric(unname(apply(compNISTHuman,2,max, na.rm=T))[7])
output$NISTHumanCOV_STD_np <- renderPlotly({
if (input$cov_std == "Coefficient of variation"){
plot_ly(compNISTHuman_nist$data_NIST) %>%
add_trace(compNISTHuman_nist$data_NIST, x = ~Mean, y = ~100*Std/Mean, color = ~Site_name,
colors = c('blue','red'), type = 'scatter', mode = 'markers', marker = list(size = ~szSample*30/maxSampleSize),
hoverinfo = 'text',
text = ~paste('<br> CoV (%): ', signif(100*Std/Mean,4),
'<br> STD (ms): ', signif(Std,4),
'<br> Mean (ms): ', signif(Mean,5),
'<br> Reference T1 (ms): ', signif(t1ROI,5),
'<br> Sample size: ', szSample,
'<br> Site ID: ', Site)) %>%
layout(xaxis = list(title=list(text="Mean value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(300,maxX+100)),
yaxis = list(title=list(text="Coefficient of variation (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,25))
)
}
else if (input$cov_std == "Standard deviation"){
plot_ly(compNISTHuman_nist$data_NIST) %>%
add_trace(compNISTHuman_nist$data_NIST, x = ~Mean, y = ~Std, color = ~Site_name,
colors = c('blue','red'), type = 'scatter', mode = 'markers', marker = list(size = ~szSample*30/maxSampleSize),
hoverinfo = 'text',
text = ~paste('<br> STD (ms): ', signif(Std,4),
'<br> Mean (ms): ', signif(Mean,5),
'<br> CoV (%): ', signif(100*Std/Mean,4),
'<br> Reference T1 (ms): ', signif(t1ROI,5),
'<br> Sample size: ', szSample,
'<br> Site ID: ', Site)) %>%
layout(xaxis = list(title=list(text="Mean value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,maxX+100)),
yaxis = list(title=list(text="Standard deviation (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,maxY+100)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.6, y=0.95, bgcolor = "rgba(0,0,0,0)"))
}
})
output$NISTHumanCOV_STD_h <- renderPlotly({
if (input$cov_std == "Coefficient of variation"){
plot_ly(compNISTHuman_human$data_human) %>%
add_trace(compNISTHuman_human$data_human, x = ~Mean, y = ~100*Std/Mean, color = ~Site_name,
colors = c('blue','red'), type = 'scatter', mode = 'markers', marker = list(size = ~szSample*30/maxSampleSize),
hoverinfo = 'text',
text = ~paste('<br> CoV (%): ', signif(100*Std/Mean,4),
'<br> STD (ms): ', signif(Std,4),
'<br> Mean (ms): ', signif(Mean,5),
'<br> ROI: ', t1ROI,
'<br> Sample size: ', szSample,
'<br> Site ID: ', Site)) %>%
layout(xaxis = list(title=list(text="Mean value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(300,maxX+100)),
yaxis = list(title=list(text="Coefficient of variation (%)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,25))
)
}
else if (input$cov_std == "Standard deviation"){
plot_ly(compNISTHuman_human$data_human) %>%
add_trace(compNISTHuman_human$data_human, x = ~Mean, y = ~Std, color = ~Site_name,
colors = c('blue','red'), type = 'scatter', mode = 'markers', marker = list(size = ~szSample*30/maxSampleSize),
hoverinfo = 'text',
text = ~paste('<br> STD (ms): ', signif(Std,4),
'<br> Mean (ms): ', signif(Mean,5),
'<br> CoV (%): ', signif(100*Std/Mean,4),
'<br> ROI: ', t1ROI,
'<br> Sample size: ', szSample,
'<br> Site ID: ', Site)) %>%
layout(xaxis = list(title=list(text="Mean value (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,maxX+100)),
yaxis = list(title=list(text="Standard deviation (ms)", font=list(size=18)), tickfont=list(size=15),
zeroline=F, showline=T, linewidth=2, linecolor="black", mirror=T, showgrid=F, range=list(0,maxY+100)),
legend = list(title=list(text="<b>Site ID</b>"), x=0.6, y=0.95, bgcolor = "rgba(0,0,0,0)"))
}
})
}