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server.R
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# Shiny Ciona Server
library('shiny')
library('Seurat')
library('RColorBrewer')
library('gplots')
source("./functions.R")
load("./temporal.Robj")
load("./spatial.Robj")
heartGene=rownames(subset(read.table("./panHP_20.markers.txt"), power>0.5 & avg_diff>1))
asmGene=rownames(subset(read.table("./ASM_20.markers.txt"), power>0.5 & avg_diff>1))
shpSpecific=rownames(subset(read.table("./SHPspecific_20.markers.txt"),power>0.5&avg_diff>1))
fhpSpecific=rownames(subset(read.table("./FHPspecific_20.markers.txt"),power>0.5&avg_diff>1))
shinyServer(function(input, output) {
genes <- reactive({
unlist(strsplit(input$genes,"\\, |\\,| "))
})
geneNames <- reactive({
unlist(strsplit(input$geneHeatmap,"\\, |\\,| "))
})
trajectObj <- reactive({
as.character(input$trajectory)
})
hpfgeneList <- reactive({
switch(input$hpfgeneList,
All = c(heartGene[1:15], fhpSpecific[1:15], shpSpecific,asmGene[1:15]),
ASM = asmGene[1:15],
Heart = heartGene[1:15],
FHP_Specific = fhpSpecific[1:15],
SHP_Specific = shpSpecific)
})
geneList <- reactive({
switch(input$geneList,
ASM = asmGene[1:15],
Heart = heartGene[1:15],
FHP_Specific = fhpSpecific[1:15],
SHP_Specific = shpSpecific)
})
trajectory <- reactive({
switch(input$trajectory,
ASM = "asm.test",
FHP = "fhp.test",
SHP = "shp.test")
})
datasetInput <-reactive({
switch(input$dataset,
ASM = "ASM_20.markers.txt",
Heart = "panHP_20.markers.txt",
FHP = "FHPspecific_20.markers.txt",
SHP = "SHPspecific_20.markers.txt",
KH2013_UniqueNAME = "KH2013_UniqueNAME.txt"
)
})
output$tsne <- renderPlot({
TSNEPlot(hpf20,do.label = T,colors.use = c("red","orange","lightblue","blue"),pt.size = 1.5)
})
output$featurePlot <- renderPlot({
if(length(genes()) != 0){
if(length(genes()) == 1){
FeaturePlot(hpf20,features.plot = genes(), nCol = 1,pt.size = 1.5)
} else{
FeaturePlot(hpf20,features.plot = genes(),pt.size = 1.5)
}
}
})
output$violinPlot <- renderPlot({
if(length(genes()) != 0){
VlnPlot(hpf20, genes(),cols.use = c("red","orange","lightblue","blue"),size.x.use = 0.8)
}
})
output$hpfheatmap <- renderPlot({
if(length(genes())==0){
if(input$hpfgeneList=="All"){
DoHeatmap(hpf20,genes.use = hpfgeneList(),order.by.ident = T,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", RowSideColors = c(rep("pink",15),rep("red",15),rep("orange",4),rep("blue",15)), key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,0.2),srtCol=0,cex.col = 1,cexRow=0.7,keysize=1,density.info=c("none"))
} else {
DoHeatmap(hpf20,genes.use = hpfgeneList(),order.by.ident = T,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,0.2),srtCol=0,cex.col = 1,cexRow=0.7,keysize=1,density.info=c("none"))
}
} else {
if(length(genes()) == 1){
heatmap.2(rbind([email protected][genes(),order(hpf20@ident)],
[email protected][genes(),order(hpf20@ident)]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = genes(),col=col,
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(hpf20@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",50),"20FHP",rep("",80),"20SHP",rep("",100),"20ASM1",
rep("",50),"20ASM2"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
DoHeatmap(hpf20,genes.use = genes(),order.by.ident = T,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),srtCol=0,cex.col = 1,cexRow=1,keysize=1,density.info=c("none"))
}
}
})
output$heatmap <- renderPlot({
if(length(geneNames()) == 0){
if(input$trajectory == "SHP"){
if(input$smooth){
heatmap.2(as.matrix([email protected][geneList(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneList(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(shp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",20),"TVC",rep("",50),"STVC",rep("",55),"SHP1",
rep("",70),"SHP2"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
DoHeatmap(shp.test,genes.use = geneList(),order.by.ident = F,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),srtCol=0,cex.col =1,cexRow=1,keysize=1,density.info=c("none"))
}
}
if(input$trajectory == "FHP"){
if(input$smooth){
heatmap.2(as.matrix([email protected][geneList(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneList(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(fhp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",35),"TVC",rep("",90),"FHP1",rep("",120),"FHP2",
rep("",100),"FHP3"),srtCol=0,cexCol=1,cexRow=1,density.info=c("none"))
} else {
DoHeatmap(fhp.test,genes.use = geneList(),order.by.ident = F,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),srtCol=0,cex.col=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
if(input$trajectory == "ASM"){
if(input$smooth){
heatmap.2(as.matrix([email protected][geneList(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneList(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(asm.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",30),"TVC",rep("",80),"STVC",rep("",90),"ASM1",
rep("",80),"ASM2",rep("",55),"ASM3"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
DoHeatmap(asm.test,genes.use = geneList(),order.by.ident = F,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),srtCol=0,cex.col=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
} else {
if(length(geneNames()) == 1){
if(input$trajectory == "SHP"){
if(input$smooth){
heatmap.2(as.matrix(rbind([email protected][geneNames(),],
[email protected][geneNames(),])),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(shp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",20),"TVC",rep("",50),"STVC",rep("",55),"SHP1",
rep("",70),"SHP2"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
heatmap.2(rbind([email protected][geneNames(),],
[email protected][geneNames(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col,
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(shp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",20),"TVC",rep("",50),"STVC",rep("",55),"SHP1",
rep("",70),"SHP2"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
if(input$trajectory == "FHP"){
if(input$smooth){
heatmap.2(as.matrix(rbind([email protected][geneNames(),],
[email protected][geneNames(),])),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(fhp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",35),"TVC",rep("",90),"FHP1",rep("",120),"FHP2",
rep("",100),"FHP3"),srtCol=0,cexCol=1,cexRow=1,density.info=c("none"))
} else {
heatmap.2(rbind([email protected][geneNames(),],
[email protected][geneNames(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col,colsep = cumsum(table(fhp.test@ident)),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
sepcolor="black",sepwidth = c(2,1),labCol=c(rep("",35),"TVC",
rep("",90),"FHP1",rep("",120),"FHP2",rep("",100),"FHP3"),
srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
if(input$trajectory == "ASM"){
if(input$smooth){
heatmap.2(as.matrix(rbind([email protected][geneNames(),],
[email protected][geneNames(),])),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(asm.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",30),"TVC",rep("",80),"STVC",rep("",90),"ASM1",
rep("",80),"ASM2",rep("",55),"ASM3"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
heatmap.2(rbind([email protected][geneNames(),],
[email protected][geneNames(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col,sepcolor = "black",colsep = cumsum(table(asm.test@ident)),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),sepwidth = c(2,1),
labCol=c(rep("",30),"TVC",rep("",80),"STVC",rep("",90),"ASM1",
rep("",80),"ASM2",rep("",55),"ASM3"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
} else {
if(input$trajectory == "SHP"){
if(input$smooth){
heatmap.2(as.matrix([email protected][geneNames(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(shp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",20),"TVC",rep("",50),"STVC",rep("",55),"SHP1",
rep("",70),"SHP2"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
DoHeatmap(shp.test,genes.use = geneNames(),order.by.ident = F,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),labCol=c(rep("",20),"TVC",rep("",50),"STVC",rep("",55),"SHP1",
rep("",70),"SHP2"),srtCol=0,cex.col=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
if(input$trajectory == "FHP"){
if(input$smooth){
heatmap.2(as.matrix([email protected][geneNames(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(fhp.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",35),"TVC",rep("",90),"FHP1",rep("",120),"FHP2",
rep("",100),"FHP3"),srtCol=0,cexCol=1,cexRow=1,density.info=c("none"))
} else {
DoHeatmap(fhp.test,genes.use = geneNames(),order.by.ident = F,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),srtCol=0,cex.col=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
if(input$trajectory == "ASM"){
if(input$smooth){
heatmap.2(as.matrix([email protected][geneNames(),]),
Rowv = NA, Colv = NA, trace = "none",
key = T,labRow = geneNames(),col=col, breaks = unique(c(seq(0,2,length=200),seq(2,6,length=200))),
key.title = "Expression Level Scale", key.xlab = "", mar=c(8,8),
colsep = cumsum(table(asm.test@ident)),sepcolor = "black",sepwidth = c(2,1),
labCol=c(rep("",30),"TVC",rep("",80),"STVC",rep("",90),"ASM1",
rep("",80),"ASM2",rep("",55),"ASM3"),srtCol=0,cexCol=1,cexRow=1,keysize=1,density.info=c("none"))
} else {
DoHeatmap(asm.test,genes.use = geneNames(),order.by.ident = F,
slim.col.label = T,draw.line = T,key.title = "Expression Level Scale",
key.xlab = "", key.ylab = "", mar=c(8,8),col=col,sepcolor="black",
sepwidth = c(1,1),srtCol=0,cex.col=1,cexRow=1,keysize=1,density.info=c("none"))
}
}
}
}
})
output$genePlot <- renderPlot({
if(length(geneNames()) == 0){
if(trajectObj() == "ASM"){
genes.plot.pseudo(eval(as.name(trajectory())),genes.use = geneList(), lwd=1.5, name.x = "ASM",inset=c(0,-0.1))
abline(v=ps.asm,lwd=2,lty=2)
}
if(trajectObj() == "FHP"){
genes.plot.pseudo(eval(as.name(trajectory())),genes.use = geneList(), lwd=1.5, name.x = "FHP",inset=c(0,-0.1))
abline(v=ps.fhp,lwd=2,lty=2)
}
if(trajectObj() == "SHP"){
genes.plot.pseudo(eval(as.name(trajectory())),genes.use = geneList(), lwd=1.5, name.x = "SHP",inset=c(0,-0.1))
abline(v=ps.shp,lwd=2,lty=2)
}
} else {
if(length(geneNames()) == 1){
if(trajectObj() == "ASM"){
genePlot.pseudo(eval(as.name(trajectory())),gene=geneNames(),col.use = c("green","yellow","lightblue","blue1","blue4"),do.spline = T,name.x = "ASM Trajectory",
cex.use = 0.8,cex.lab=1,do.logit = T)
abline(v=ps.asm,lwd=2,lty=2)
}
if(trajectObj() == "FHP"){
genePlot.pseudo(eval(as.name(trajectory())),gene=geneNames(),col.use = c("green","pink1","red1","red4"),do.spline = T,name.x = "FHP Trajectory",
cex.use = 0.8,cex.lab=1,do.logit = T)
abline(v=ps.fhp,lwd=2,lty=2)
}
if(trajectObj() == "SHP"){
genePlot.pseudo(eval(as.name(trajectory())),gene=geneNames(),col.use = c("green","yellow","orange1","orange4"),do.spline = T,name.x = "SHP Trajectory",
cex.use = 0.8,cex.lab=1,font.lab=2,do.logit = T)
abline(v=ps.shp,lwd=2,lty=2)
}
} else {
if(trajectObj() == "ASM"){
genes.plot.pseudo(eval(as.name(trajectory())),genes.use = geneNames(), lwd=1.5, name.x = "ASM",inset=c(0,-0.1))
abline(v=ps.asm,lwd=2,lty=2)
}
if(trajectObj() == "FHP"){
genes.plot.pseudo(eval(as.name(trajectory())),genes.use = geneNames(), lwd=1.5, name.x = "FHP",inset=c(0,-0.1))
abline(v=ps.fhp,lwd=2,lty=2)
}
if(trajectObj() == "SHP"){
genes.plot.pseudo(eval(as.name(trajectory())),genes.use = geneNames(), lwd=1.5, name.x = "SHP",inset=c(0,-0.1))
abline(v=ps.shp,lwd=2,lty=2)
}
}
}
})
output$vlnPlot <- renderPlot({
if(length(geneNames()) != 0){
if(trajectObj() == "ASM"){
VlnPlot(eval(as.name(trajectory())), geneNames(),cols.use = c("green","yellow","lightblue","blue1","blue4"),size.x.use = 8)
}
if(trajectObj() == "FHP"){
VlnPlot(eval(as.name(trajectory())), geneNames(),cols.use = c("green","pink","red1","red4"),size.x.use = 8)
}
if(trajectObj() == "SHP"){
VlnPlot(eval(as.name(trajectory())), geneNames(),cols.use = c("green","yellow","orange1","orange4"),size.x.use = 8)
}
}
})
output$downloadData <- downloadHandler(
filename = function(){paste(input$dataset,"txt",sep = ".")},
content = function(file){file.copy(datasetInput(),file)},
contentType = "text/plain"
)
})