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Commit 5c6567cc authored by Todor Kondic's avatar Todor Kondic
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Merge branch 'devel' into 'master' 

Devel

See merge request !11
parents b448d285 e0d5716c
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with 53 additions and 33 deletions
R/mix.R
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− 33
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......@@ -483,9 +483,8 @@ arrPlot <- function(xlim,ylim,ytics,xaxis=F,log=NULL,cex=0.2) {
}
arrPlotStd <- function(xlim,ylim,xaxis=F,log="",cex=1.5,mar) {
if (ylim[1]<1) ylim[1] <- 1
arrPlotStd <- function(xlim,ylim,xaxis=F,log=log,cex=1.5,mar,intTresh) {
if (ylim[1]<intTresh) ylim[1] <- intTresh
if (is.na(ylim[2])) ylim[2] <- 10
if (xaxis) xaxt="s" else xaxt="n"
par(mar=mar)
......@@ -496,12 +495,11 @@ arrPlotStd <- function(xlim,ylim,xaxis=F,log="",cex=1.5,mar) {
ltics <- calcLabels(ytics)
axis(side=2,at=ytics,labels=ltics,las=2,cex.axis=cex,gap.axis = -1)
}
plot_id_aux <- function(i,wd,eics,maybekids,masses,osmesi,tags,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,rtrange=NULL) {
plot_id_aux <- function(i,wd,eics,maybekids,masses,osmesi,tags,logYAxis,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4,rtrange=NULL) {
clean_rtrange <- function(def) {
x1 <- rtrange[1]
x2 <- rtrange[2]
......@@ -510,7 +508,14 @@ plot_id_aux <- function(i,wd,eics,maybekids,masses,osmesi,tags,pal="Dark2",cex=0
c(x1,x2)
}
#LEFT_MARGIN=11
if (logYAxis == "linear") log = ""
if (logYAxis == "log") log = "y"
LEFT_MARGIN=9
eic <- eics[[i]]
maybekid <- maybekids[[i]]
......@@ -558,7 +563,8 @@ plot_id_aux <- function(i,wd,eics,maybekids,masses,osmesi,tags,pal="Dark2",cex=0
## par(mar=c(1,2,1,4))
struc_xr <- c(0,100)
struc_yr <- c(0,100)
par(mar=c(1,9,3,4))
par(mar=c(1,LEFT_MARGIN,3,4))
plot(1,1,type="n",xlab="",ylab="",xlim=struc_xr,ylim=struc_yr,xaxt="n",yaxt="n",asp=1,axes = FALSE)
rendersmiles2(osmesi[i],coords=c(struc_xr[1],struc_yr[1],struc_xr[2],struc_yr[2]))
......@@ -571,10 +577,11 @@ plot_id_aux <- function(i,wd,eics,maybekids,masses,osmesi,tags,pal="Dark2",cex=0
cols_kids <- cols[indkids]
lgnd_kids <- Map(function(k,v) paste(k,"= ",formatC(v,digits=rt_digits,format="f"),sep=''),symbs_kids,rt_max_kids)
if (length(lgnd_kids)>0) legend(x=linfo$rect$left-14*linfo$rect$left,y=linfo$rect$top-1*linfo$rect$h,horiz=F,legend=lgnd_kids,fill=cols[indkids],bty="n",cex=1.5)
arrPlotStd(xlim=rt_rng,ylim=int_rng,mar=c(0,9,3,0),log="")
arrPlotStd(xlim=rt_rng,ylim=int_rng,mar=c(0,LEFT_MARGIN,3,0),log=log,intTresh=1e4)
title(main=paste("ID:",i,"Ion m:",formatC(masses[[i]],digits=m_digits,format="f")))
for (k in seq(length(w_max))) text(rt_max[[k]],i_max[[k]],labels=symbs[[k]],pos=4,offset=0.5*k)
......@@ -588,12 +595,12 @@ plot_id_aux <- function(i,wd,eics,maybekids,masses,osmesi,tags,pal="Dark2",cex=0
if (length(dfs_kids) >0) {
arrPlotStd(xlim=rt_rng,ylim=int_rng_kids,xaxis=T,log="y",mar=c(4,9,0,0))
arrPlotStd(xlim=rt_rng,ylim=int_rng_kids,xaxis=T,log=log,mar=c(4,LEFT_MARGIN,0,0),intTresh=1)
for (k in 1:length(indkids)) {
lines(intensity ~ rt,data=dfs_kids[[k]],type="h",col=cols_kids[[k]])
}
} else {
arrPlotStd(xlim=rt_rng,ylim=c(1,10),xaxis=T,log="y",mar=c(4,9,0,0))
arrPlotStd(xlim=rt_rng,ylim=c(1,10),xaxis=T,log=log,mar=c(4,9,0,0),intTresh=1)
}
mtext("retention time [min]",side = 1,adj=0.5,cex=1.3,line = 3)
if (length(dfs_kids)>0) for (k in seq(length(w_max_kids))) text(rt_max_kids[[k]],i_max_kids[[k]],labels=symbs_kids[[k]],pos=4,offset=0.5*k)
......@@ -646,7 +653,7 @@ presc.plot <- function(prescdf,mode,out="prescreen.pdf",fn_cmpd_l,pal="Dark2",ce
maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')})
pdf(out)
for (i in 1:length(osmesi)) plot_id_aux(i=i,wd=wd,eics=eics,maybekids=maybekids,masses=masses,osmesi=osmesi,tags=tags,rtrange=rtrange,cex=cex,pal=pal,rt_digits=rt_digits,m_digits=m_digits)
for (i in 1:length(osmesi)) plot_id_aux(i=i,wd=wd,eics=eics,maybekids=maybekids,masses=masses,osmesi=osmesi,log="y",tags=tags,rtrange=rtrange,cex=cex,pal=pal,rt_digits=rt_digits,m_digits=m_digits)
dev.off()
}
......@@ -665,7 +672,7 @@ mkUI <- function(idSliderRange,setName,rtRange,tags) {
nvPanel <- do.call(shiny::navlistPanel, tabPanelList)
ui <- shinydashboard::dashboardPage(
ui <- shinydashboard::dashboardPage(skin="black",
shinydashboard::dashboardHeader(title = "Prescreening"),
shinydashboard::dashboardSidebar(
width = 350,
......@@ -673,6 +680,7 @@ mkUI <- function(idSliderRange,setName,rtRange,tags) {
shinydashboard::sidebarSearchForm(textId = "searchText", buttonId = "searchButton", label = "Search..."),
shinydashboard::menuItem(text = "Dashboard", tabName = "Dashboard", icon = shiny::icon("dashboard")))),
shinydashboard::dashboardBody(
shiny::fluidRow(
shinydashboard::box(
title = "MS Prescreening", width = 7, height = "80px", background = "blue", ""
......@@ -684,34 +692,39 @@ mkUI <- function(idSliderRange,setName,rtRange,tags) {
),
shiny::fluidRow(
shinydashboard::box(
title = "Plot", width = 7, solidHeader = TRUE, collapsible = TRUE,
title = "Plot", width = 7, color = "olive", solidHeader = FALSE, collapsible = TRUE,
shiny::plotOutput("plot1", width = "100%", height = "750px", click = NULL,
dblclick = NULL, hover = NULL, hoverDelay = NULL,
hoverDelayType = NULL, brush = NULL, clickId = NULL,
hoverId = NULL),
shiny::textInput("plotname", "Insert plot name: (e.g. plotname_%i.pdf)",value="plotCpdID_%i.pdf"),
shiny::actionButton("saveplot", "Save", icon = shiny::icon("save")),
shiny::actionButton("saveallplots", "Save All", icon = shiny::icon("save"))
shiny::actionButton("saveallplots", "Save All Plots", icon = shiny::icon("save"))
),
shinydashboard::box(
title = "Compounds", width=5,solidHeader = TRUE, collapsible = TRUE, "", shiny::br(),
title = "Compounds", width=5, solidHeader = FALSE, color = "olive", collapsible = TRUE, "", shiny::br(),
shiny::sliderInput("idslider", "Compound number:", idSliderRange[1], idSliderRange[2], value=1,step=1)
),
shinydashboard::box(
title = "Plot x axis range", width = 5, solidHeader = TRUE, collapsible = TRUE,
shiny::numericInput("min_val", "Minimum x Axis Value", rtRange[1]),
shiny::numericInput("max_val", "Maximum x Axis Value", rtRange[2])
),
shinydashboard::box(
title = "Prescreening analysis", width = 5, solidHeader = TRUE, collapsible = TRUE,
title = "Prescreening analysis", width = 5, solidHeader = FALSE, collapsible = TRUE,
shiny::titlePanel(setName),
nvPanel,
shiny::actionButton("submitQA", "Submit", icon = shiny::icon("save")),
shiny::textInput("fn_ftable", "File table Name",value="ftable.csv"),
shiny::actionButton("savefiletable", "Save File Table")
)
)
shiny::actionButton("savefiletable", "Save File Table", icon = shiny::icon("save"))
),
shinydashboard::box(
title = "Plot Parameters", width=7, solidHeader = FALSE, collapsible = TRUE, "", shiny::br(),
shiny::numericInput("min_val", "Minimum x Axis Value", rtRange[1]),
shiny::numericInput("max_val", "Maximum x Axis Value", rtRange[2]),
shiny::radioButtons("yaxis", "Parameters for y Axis",
c(linear = "linear",
log = "log")),
shiny::numericInput("nice", "Nice", rtRange[1]),
shiny::numericInput("steps", "Steps", rtRange[2])
)
)
)
)}
......@@ -782,7 +795,7 @@ presc.shiny <-function(prescdf,mode,fn_cmpd_l,pal="Dark2",cex=0.75,rt_digits=2,m
eics <- list.files(path=wd[[1]],patt=".*eic.csv")
maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')})
plot_id <- function (i,rtrange) plot_id_aux(i=i,wd=wd,eics=eics,maybekids=maybekids,masses=masses,osmesi=osmesi,tags=tags,rtrange=rtrange,cex=cex,pal=pal,rt_digits=rt_digits,m_digits=m_digits)
plot_id <- function (i,rtrange,log=rv$yaxis) plot_id_aux(i=i,wd=wd,eics=eics,maybekids=maybekids,masses=masses,osmesi=osmesi,tags=tags,log=log,rtrange=rtrange,cex=cex,pal=pal,rt_digits=rt_digits,m_digits=m_digits)
......@@ -812,11 +825,13 @@ presc.shiny <-function(prescdf,mode,fn_cmpd_l,pal="Dark2",cex=0.75,rt_digits=2,m
no_cmpds=no_cmpds)
output$plot1 <- renderPlot(
{
i=input$idslider
{ i=input$idslider
rtrange <- c(input$min_val,input$max_val)
plot_id(i,rtrange=rtrange, log=input$yaxis)
rtrange <- c(input$min_val,input$max_val)
plot_id(i,rtrange=rtrange)
# intParameter <- c(input$nice, input$steps)
})
output$value <- renderText(
......@@ -837,7 +852,7 @@ presc.shiny <-function(prescdf,mode,fn_cmpd_l,pal="Dark2",cex=0.75,rt_digits=2,m
fn <- sprintf(pfn,i)
rtrange <- c(input$min_val,input$max_val)
pdf(file=fn, width=12, height=8)
plot_id(i,rtrange=rtrange)
plot_id(i,rtrange=rtrange, log=input$yaxis)
dev.off()
})
......@@ -849,7 +864,7 @@ presc.shiny <-function(prescdf,mode,fn_cmpd_l,pal="Dark2",cex=0.75,rt_digits=2,m
fn <- sprintf(pfn,i)
pdf(file=fn, width=12, height=8)
for (i in 1:rv$no_cmpds) {
plot_id(i)
plot_id(i,log=input$yaxis)
message("Compound ID ",i," done.")
}
dev.off()
......@@ -861,6 +876,11 @@ presc.shiny <-function(prescdf,mode,fn_cmpd_l,pal="Dark2",cex=0.75,rt_digits=2,m
rv$prescdf <- updateFileTable(df=rv$prescdf,id=input$idslider,linput=res)
})
## shiny::observeEvent(input$yaxis,{
## rv$yaxis <- input$yaxis
## })
shiny::observe({
i <- input$idslider
sdf <- queryFileTable(df=rv$prescdf,id=i)
......
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