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Merge pull request #24 from marcos-diazg/mdiaz-dev
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Mdiaz dev
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Marcos Díaz-Gay authored Nov 29, 2017
2 parents ed9896b + a499a1e commit 0e4b18e
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Showing 2 changed files with 60 additions and 85 deletions.
143 changes: 58 additions & 85 deletions server.R
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Original file line number Diff line number Diff line change
Expand Up @@ -231,23 +231,13 @@ shinyServer(function(input, output,session){
selectInput("mysamp","Select your samples",mysamp, multiple=TRUE, selectize = FALSE, size=1, selected=colnames(as.data.frame(fit_res()$contribution)))
} else {

if (input$tab == "96prof" | input$tab == "pca"){

if (input$tab=="reconst"){
mysamp<-colnames(as.data.frame(fit_res()$contribution))
selectInput("mysamp","Select your samples",mysamp, multiple=TRUE, selectize = FALSE, size=6, selected = mysamp[1])
} else {
mysamp<-c("All samples",colnames(as.data.frame(fit_res()$contribution)))
selectInput("mysamp","Select your samples",mysamp, multiple=TRUE, selectize = FALSE, size=6, selected="All samples")

} else {

if (input$tab=="reconst"){
mysamp<-colnames(as.data.frame(fit_res()$contribution))
selectInput("mysamp","Select your samples",mysamp, multiple=TRUE, selectize = FALSE, size=6, selected = mysamp[1])
} else {

mysamp<-c("All samples","All samples + mean",colnames(as.data.frame(fit_res()$contribution)),"mean")
selectInput("mysamp","Select your samples",mysamp, multiple=TRUE, selectize = FALSE, size=6, selected="All samples")
}
}

}
})

Expand All @@ -261,68 +251,60 @@ shinyServer(function(input, output,session){

})

#Checkbox to decide if mean is plotted.
output$mean_checkbox<-renderUI({
if (input$tab=="smp" | input$tab=="contrib" | input$tab=="comp_canc_sign"){
checkboxInput("meancheck","Show mean",value=FALSE)
} else {
return(invisible(NULL))
}
})




#Select which samples use to plot.
my_contributions<- reactive({

#Error management
if (length(input$mysamp)==0) return(invisible(NULL))

if ("All samples + mean" %in% input$mysamp) {
aux<-divisionRel(as.data.frame(fit_res()$contribution))
con<-data.frame(aux, mean = apply(aux,1,mean))
colnames(con)<-c(colnames(aux),"mean")


if ("All samples" %in% input$mysamp){
if(input$meancheck==TRUE) {
aux<-divisionRel(as.data.frame(fit_res()$contribution))
con<-data.frame(aux, mean = apply(aux,1,mean))
colnames(con)<-c(colnames(aux),"mean")
} else {
aux<-divisionRel(as.data.frame(fit_res()$contribution))
con<-data.frame(aux)
colnames(con)<-c(colnames(aux))
}

} else {
if ("All samples" %in% input$mysamp){
if("mean" %in% input$mysamp) {
aux<-divisionRel(as.data.frame(fit_res()$contribution))
con<-data.frame(aux, mean = apply(aux,1,mean))
colnames(con)<-c(colnames(aux),"mean")
} else {
aux<-divisionRel(as.data.frame(fit_res()$contribution))
con<-data.frame(aux)
colnames(con)<-c(colnames(aux))
}



if(input$meancheck==TRUE) {
aux<-divisionRel(as.data.frame(fit_res()$contribution[,input$mysamp]))
con<-data.frame(aux, mean = apply(aux,1,mean))
colnames(con)<-c(colnames(aux),"mean")
} else {

if("mean" %in% input$mysamp) {
if (length(input$mysamp)>1) {
aux<-divisionRel(as.data.frame(fit_res()$contribution[,input$mysamp[-length(input$mysamp)]]))
con<-data.frame(aux, mean = apply(aux,1,mean))
colnames(con)<-c(colnames(aux),"mean")

} else {
aux<-divisionRel(as.data.frame(fit_res()$contribution))
con<-data.frame(mean = apply(aux,1,mean))
}

} else {
aux<-divisionRel(as.data.frame(fit_res()$contribution[,input$mysamp]))
con<-data.frame(aux)
colnames(con)<-colnames(aux)
}
aux<-divisionRel(as.data.frame(fit_res()$contribution[,input$mysamp]))
con<-data.frame(aux)
colnames(con)<-colnames(aux)
}
}



#Fixing colname of one sample (without mean)
if (ncol(con)==1 & colnames(con)[1]!="mean"){
colnames(con)<-setdiff(input$mysamp,c("All samples","mean","All samples + mean"))
if (ncol(con)==1){
colnames(con)<-setdiff(input$mysamp,c("All samples"))
}

#Fixing colname of one sample (with mean)
if (ncol(con)==2 & colnames(con)[2]=="mean" & input$mysamp!="All samples + mean" & input$mysamp!="All samples"){
colnames(con)[1]<-setdiff(input$mysamp,c("All samples","mean","All samples + mean"))
if (ncol(con)==1 & input$meancheck==TRUE & input$mysamp!="All samples"){
colnames(con)[1]<-setdiff(input$mysamp,c("All samples"))
}

#Fixing colname of just mean of samples
if (ncol(con)==1 & colnames(con)[1]=="mean"){
colnames(con)<-"mean"
}

return(con)

Expand Down Expand Up @@ -360,31 +342,22 @@ shinyServer(function(input, output,session){

#Selection of samples to plot
mutation_counts<- reactive({

if ("All samples + mean" %in% input$mysamp) {
mc<-data.frame(samples=c(names(vcfs()),"mean"),smp=(c(sapply(vcfs(),length),mean(sapply(vcfs(),length))))/megabases())

} else {
if ("All samples" %in% input$mysamp){

if ("All samples" %in% input$mysamp){
if("mean" %in% input$mysamp) {
mc<-data.frame(samples=c(names(vcfs()),"mean"),smp=(c(sapply(vcfs(),length),mean(sapply(vcfs(),length))))/megabases())
} else {
mc<-data.frame(samples=names(vcfs()),smp=(sapply(vcfs(),length))/megabases())
}
if(input$meancheck==TRUE) {
mc<-data.frame(samples=c(names(vcfs()),"mean"),smp=(c(sapply(vcfs(),length),mean(sapply(vcfs(),length))))/megabases())
} else {
mc<-data.frame(samples=names(vcfs()),smp=(sapply(vcfs(),length))/megabases())
}

if("mean" %in% input$mysamp) {
if (length(input$mysamp)>1) {
aux<-input$mysamp[-length(input$mysamp)]
mc<-data.frame(samples=c(names(vcfs()[aux]),"mean"), smp=(c(sapply(vcfs()[aux],length),mean(sapply(vcfs()[aux],length))))/megabases())

} else {
mc<-data.frame(samples=c("mean"),smp=(c(mean(sapply(vcfs(),length))))/megabases())
}
} else {
mc<-data.frame(samples=names(vcfs()[input$mysamp]), smp=(sapply(vcfs()[input$mysamp],length))/megabases())
}
} else {

if(input$meancheck==TRUE) {
aux<-input$mysamp
mc<-data.frame(samples=c(names(vcfs()[aux]),"mean"), smp=(c(sapply(vcfs()[aux],length),mean(sapply(vcfs()[aux],length))))/megabases())
} else {
mc<-data.frame(samples=names(vcfs()[input$mysamp]), smp=(sapply(vcfs()[input$mysamp],length))/megabases())
}
}
return(mc)
Expand Down Expand Up @@ -447,8 +420,8 @@ shinyServer(function(input, output,session){

plot_smp + geom_bar(stat="identity",fill="orangered2") + theme_minimal() + geom_text(aes(label=smp), size=5, position = position_stack(vjust = 0.5), colour="white") + coord_flip() + labs(x = "", y = "Somatic mutation prevalence (number of mutations per megabase)") + theme(axis.text=element_text(size=12), axis.title = element_text(size = 13, face = "bold"), panel.grid.major.y=element_blank(), panel.grid.minor.y=element_blank(), panel.grid.major.x=element_blank(), panel.grid.minor.x=element_blank())

ggsave(ff,height=2*ncol(mutation_counts_new),width=10,dpi=ppi)
ggsave(ff,height=min(2*nrow(mutation_counts_new),40),width=25,dpi=ppi,units="cm")

}
)

Expand Down Expand Up @@ -500,7 +473,7 @@ shinyServer(function(input, output,session){

plot_96_profile(aux_96_profile,ymax = max_ymax) + scale_y_continuous(breaks = seq(0, max_ymax, 0.05))

ggsave(ff,height=2*ncol(aux_96_profile),width=10,dpi=ppi)
ggsave(ff,height=min(4*ncol(aux_96_profile),40),width=25,dpi=ppi,units="cm")
}
)

Expand Down Expand Up @@ -529,15 +502,15 @@ shinyServer(function(input, output,session){

#DataTable
output$contr <- renderDataTable({
data.frame(Signature = 1:30, Proposed_Etiology = proposed_etiology, my_contributions())
data.frame(Signature = 1:30, Proposed_Etiology = proposed_etiology, round(my_contributions(),3))
},
options = list(lengthChange=FALSE,pageLength=30, paging=FALSE, searching=FALSE, info=FALSE)
)


#Download Table
output$download_contr <- downloadHandler( filename="COSMIC_sign_contributions.txt", content=function (file){
write.table(x = data.frame(Signature = 1:30, Proposed_Etiology = proposed_etiology, my_contributions()), file = file, sep = "\t", quote=F, row.names=F)})
write.table(x = data.frame(Signature = 1:30, Proposed_Etiology = proposed_etiology, round(my_contributions(),3)), file = file, sep = "\t", quote=F, row.names=F)})


#check if column or row dendogram is needed
Expand Down Expand Up @@ -628,7 +601,7 @@ shinyServer(function(input, output,session){
need(length(input$mysamp)==1,"Sample selection error, please select just one sample at a time to visualize its reconstructed mutational profile.")
)

if (input$mysamp=="All samples + mean" | input$mysamp=="All samples") return(invisible(NULL))
if (input$mysamp=="All samples") return(invisible(NULL))


original_prof <- mut_mat()[,input$mysamp]
Expand Down Expand Up @@ -895,7 +868,7 @@ shinyServer(function(input, output,session){
xlim=c(min(pca$x[,1])-0.5*( max(pca$x[,1])-min(pca$x[,1]) ) ,max(pca$x[,1])+0.5*( max(pca$x[,1])-min(pca$x[,1]) ) ),
ylim=c(min(pca$x[,2])-0.5*( max(pca$x[,2])-min(pca$x[,2]) ) ,max(pca$x[,2])+0.5*( max(pca$x[,2])-min(pca$x[,2]) ) ),
main="PCA")
text(pca$x[,1], pca$x[,2]-0.15, rownames(a))
text(pca$x[,1], pca$x[,2]-0.25, rownames(a))


} else {
Expand Down
2 changes: 2 additions & 0 deletions ui.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -60,11 +60,13 @@ shinyUI(fluidPage(

#Sample selection for plots (post push run)
uiOutput("selected_samples"),
uiOutput("mean_checkbox"),

#Cancer type selection for plots (post push run)
uiOutput("selected_cancer_types"),

hr(),

uiOutput("col_dendro_heatmap"),
uiOutput("row_dendro_heatmap"),
uiOutput("col_dendro_cancers"),
Expand Down

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