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server.R
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server.R
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server <- function(input,
output,
session) {
observeEvent(input$update, {
if(!is.null(input$datafile)){
dat <- read.csv(input$datafile$datapath,
sep=";"
)
if(input$var1 == "Gfap") mark = 'gfap_only'
if(input$var1 == "Aldh1l1") mark = 'aldh_only'
if(input$var1 == "Colocalization") mark = 'both'
marker <- get.data(data=dat,
marker=mark,
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
if(input$var2 == "Chow"){
dat_mark2 = marker[[1]]
diet2 = 0
}
if(input$var2 == "HFHS 5 days"){
dat_mark2 = marker[[2]]
diet2 = 5
}
if(input$var2 == "HFHS 15 days"){
dat_mark2 = marker[[3]]
diet2 = 15
}
output$plot <- renderPlot({
if(input$analysis == "initial_visualization"){
if(input$var11 == "Gfap") mark = 'gfap_only'
if(input$var11 == "Aldh1l1") mark = 'aldh_only'
if(input$var11 == "Colocalization") mark = 'both'
marker <- get.data(data=dat,
marker=mark,
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
if(input$var21 == "Chow"){
dat_mark2 = marker[[1]]
diet2 = 0
}
if(input$var21 == "HFHS 5 days"){
dat_mark2 = marker[[2]]
diet2 = 5
}
if(input$var21 == "HFHS 15 days"){
dat_mark2 = marker[[3]]
diet2 = 15
}
p <- gg.aspp(data=dat_mark2,
type_plot=input$plt1,
title=paste(input$var11, ":", input$var21, 'diet')
)
print(p)
}
if(input$analysis == "3D_plots"){
if(input$var12 == "Gfap") mark = 'gfap_only'
if(input$var12 == "Aldh1l1") mark = 'aldh_only'
if(input$var12 == "Colocalization") mark = 'both'
marker <- get.data(data=dat,
marker=mark,
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
if(input$var22 == "Chow"){
dat_mark2 = marker[[1]]
diet2 = 0
}
if(input$var22 == "HFHS 5 days"){
dat_mark2 = marker[[2]]
diet2 = 5
}
if(input$var22 == "HFHS 15 days"){
dat_mark2 = marker[[3]]
diet2 = 15
}
if(input$plt2 == "3D_dens"){
d3.aspp(data=dat_mark2,
type_plot="3D_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
title=paste(input$var12, ":", input$var22, 'diet'),
col="greenyellow",
theta=0,
phi=60
)
} else{
if(input$plt2 == "3D_scatter"){
ps <- scatter3D(dat_mark2$X,
dat_mark2$Y,
as.numeric(as.factor(paste0(dat_mark2$Mouse, dat_mark2$ARC, dat_mark2$Diet))),
pch=20,
nticks=5,
col="cornflowerblue",
ticktype="detailed",
theta=50,
phi=5,
xlab="X",
ylab="Y",
zlab="Slides",
main="gfap",
cex=0.3
)
print(ps)
} else{
p <- d3.aspp(data=dat_mark2,
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
type_plot="3D_plot_interactive",
title="Gfap chow diet"
)
print(p)
}
}
}
if(input$analysis == "classification_plot"){
marker1 <- get.data(data=dat,
marker='gfap_only',
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
marker2 <- get.data(data=dat,
marker='aldh_only',
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
marker3 <- get.data(data=dat,
marker='both',
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
if(input$var23 == "Chow") all = rbind(marker1[[1]], marker2[[1]], marker3[[1]])
if(input$var23 == "HFHS 5 days") all = rbind(marker1[[2]], marker2[[2]], marker3[[2]])
if(input$var23 == "HFHS 15 days") all = rbind(marker1[[3]], marker2[[3]], marker3[[3]])
moran=test.saptcorr(dataX=all$X,
dataY=all$Y,
dataG=all$Gene,
method="Moran.I"
)
if(input$plt3 == "random_forest"){
theme_update(text=element_text(size=20))
pl=randF.class(dataX=all$X,
dataY=all$Y,
dataG=all$Gene) +
xlab(expression(paste("Distance ", "(", mu, "m)"))) +
ylab(expression(paste("Distance ", "(", mu, "m)"))) +
scale_fill_manual(values=c("limegreen","dodgerblue","magenta")) +
xlim(0,500) +
ylim(0,450) +
geom_text(x=350,
y=350,
label=paste("Moran.I=", as.character(round(moran$observed, 3))),
size=7
)
print(pl)
}
if(input$plt3 == "knn_network"){
theme_update(text=element_text(size=20))
pk <- plot.2d.knn(train_labels=all$Gene,
train_data=all[,6:7],
k=5,
X1="X",
X2="Y") +
annotate("text",
x=400,
y=400,
label=paste("Moran.I=", as.character(round(t$observed, 3))),
size=6) +
xlab(expression(paste("Distance ", "(", mu, "m)"))) +
ylab(expression(paste("Distance ", "(", mu, "m)")))
print(pk)
}
}
if(input$analysis == "density_test_plots"){
if(input$var1 == "Gfap") mark = 'gfap_only'
if(input$var1 == "Aldh1l1") mark = 'aldh_only'
if(input$var1 == "Colocalization") mark = 'both'
marker <- get.data(data=dat,
marker=mark,
diet=c(0, 5, 15),
mouse=1:4,
arc=1:8,
cal_arc=FALSE
)
if(input$var2 == "Chow"){
dat_mark2 = marker[[1]]
diet2 = 0
}
if(input$var2 == "HFHS 5 days"){
dat_mark2 = marker[[2]]
diet2 = 5
}
if(input$var2 == "HFHS 15 days"){
dat_mark2 = marker[[3]]
diet2 = 15
}
if(input$var3 == "Chow"){
dat_mark3 = marker[[1]]
diet3 = 0
}
if(input$var3 == "HFHS 5 days"){
dat_mark3 = marker[[2]]
diet3 = 5
}
if(input$var3 == "HFHS 15 days"){
dat_mark3 = marker[[3]]
diet3 = 15
}
if(input$plt == "square_plot"){
if(input$var3 == "none"){
dens.aspp(data=dat_mark2,
type_plot="subtraction_square_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
nr_sq=input$num_sqr_x,
title=paste(input$var1, ":", input$var2, 'diet'),
col=c("grey", "firebrick2", "yellow"),
ribbon=input$ribbon,
contour=input$contours,
)
} else{
dens.aspp(data=dat_mark2,
data1=dat_mark3,
type_plot="subtraction_square_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
nr_sq=input$num_sqr_x,
title=paste(input$var1, ":", input$var2, 'vs.', input$var3, 'diet'),
col=c("blue", "grey", "firebrick2"),
ribbon=input$ribbon,
contour=input$contours
)
}
}
if(input$plt == "density_plot"){
if(input$var3 == "none"){
dens.aspp(data=dat_mark2,
type_plot="subtraction_dens_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
nr_sq=input$num_sqr_x,
title=paste(input$var1, ":", input$var2, 'diet'),
col=c("yellow", "firebrick2", "grey"),
ribbon=input$ribbon,
contour=input$contours,
)
} else{
dens.aspp(data=dat_mark2,
data1=dat_mark3,
type_plot="subtraction_dens_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
nr_sq=input$num_sqr_x,
title=paste(input$var1, ":", input$var2, 'vs.', input$var3, 'diet'),
col=c("blue", "grey", "firebrick2"),
ribbon=input$ribbon,
contour=input$contours
)
}
}
if(input$plt == "test_plot"){
if(input$var3 == "none"){
dens.aspp(data=dat_mark2,
type_plot="test_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
nr_sq=input$num_sqr_x,
title=paste(input$var1, ":", input$var2, 'vs.', input$var3, 'diet'),
col=c("grey", "firebrick2", "yellow"),
ribbon=input$ribbon,
contour=input$contours,
cex.axis=1.5,
cex.lab=1.2
)
} else{
alt <- get.data(data=dat,
marker=mark,
diet=diet3,
mouse=1:4,
arc=1:8,
cal_arc=TRUE
)
nul <- get.data(data=dat,
marker=mark,
diet=diet2,
mouse=1:4,
arc=1:8,
cal_arc=TRUE
)
dens.aspp(data=dat_mark2,
data1=dat_mark3,
test_null=nul,
test_alt=alt,
type_plot="subtraction_dens_plot",
window=owin(poly=list(x=c(0, 500, 0), y=c(0, 0, 500))),
nr_sq=input$num_sqr_x,
title=paste(input$var1, ":", input$var2, 'vs.', input$var3, 'diet'),
col=c("blue", "grey", "firebrick2"),
ribbon=input$ribbon,
contour=input$contours,
cex.axis=1.2,
cex.lab=1.2
)
}
}
}
})
}
})
}