Skip to content
Snippets Groups Projects
Commit 907e4903 authored by Jessy Krier's avatar Jessy Krier
Browse files

Shiny minimal implementation works

parent 5f4a2ba2
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
DESCRIPTION
+ 3
− 1
View file @ 907e4903
......@@ -27,4 +27,6 @@ Imports:
yaml,
mzR,
RColorBrewer,
curl
curl,
shiny,
shinydashboard
NAMESPACE
+ 1
− 0
View file @ 907e4903
......@@ -5,3 +5,4 @@ export(mb.prep)
export(presc.do)
export(presc.plot)
export(sw.do)
export(presc.shiny)
R/mix.R
+ 180
− 0
View file @ 907e4903
......@@ -514,4 +514,184 @@ mb.p<-function(mb,infodir,fn_stgs,cl=F) {
names(x)<-names(mb)
x}
##' Prescreening using shiny interface.
##'
##' @title Prescreening with Shiny
##' @return Nothing useful.
##' @author Jessy Krier
##' @author Mira Narayanan
presc.shiny <-function(wd,mode,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
modemap=list(pH="MpHp_mass",
mH="MmHm_mass",
blahnh4="MpNH4_mass",
blahna="MpNa_mass")
dfdir <- file.path(wd,"prescreen")
wd1 <- wd[[1]]
df <- read.csv(file=get_cmpd_l_fn(wd1),stringsAsFactors = F)
osmesi <- df$SMILES
no_cmpds <- length(osmesi)
# reconf(wd1)
masses <- lapply(osmesi,function (smile) {
#osmesi <- tryCatch(RMassBank::findSmiles(i), error = function(e) NA)
zz <- RChemMass::getSuspectFormulaMass(smile)
zz[[modemap[[mode]]]]
})
#message("Masses:",masses)
# return(osmesi)
## Get the basenames of eic files.
eics <- list.files(path=dfdir[[1]],patt=".*eic.csv")
maybekids <- sapply(strsplit(eics,split="\\."),function(x) {paste(x[[1]][1],'.kids.csv',sep='')})
idsliderrange <- range(df$ID)
ui <- shinydashboard::dashboardPage(
shinydashboard::dashboardHeader(title = "Prescreening"),
shinydashboard::dashboardSidebar(
width = 350,
shinydashboard::sidebarMenu(
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 = 6, background = "blue", ""
),
shinydashboard::box(
title = "ID N°",width = 6, background = "maroon", ""
)
),
shiny::fluidRow(
shinydashboard::box(
title = "Plot", width = 6, solidHeader = TRUE, collapsible = TRUE,
plotOutput("plot1", width = "100%", height = "400px", click = NULL,
dblclick = NULL, hover = NULL, hoverDelay = NULL,
hoverDelayType = NULL, brush = NULL, clickId = NULL,
hoverId = NULL)
),
shinydashboard::box(
title = "Compounds", solidHeader = TRUE, collapsible = TRUE, "", br(),
sliderInput("idslider", "Compound number:", idsliderrange[1], idsliderrange[2], value=1,step=1)
)
),
shiny::fluidRow(
shinydashboard::box(
title = "Plot x axis range", width = 6, solidHeader = TRUE, collapsible = TRUE,
shinyUI(pageWithSidebar(
headerPanel(""),
sidebarPanel(
numericInput("min_val", "Minimum x Axis Value", 1),
numericInput("max_val", "Maximum x Axis Value", 100),
uiOutput("slider")),
mainPanel()
))
),
shinydashboard::box(
title = "Prescreening Results", width = 6, solidHeader = TRUE, collapsible = TRUE,
checkboxGroupInput("variable", "Checkboxes:",
c("MS1" = "MS1 present",
"MS2" = "MS2 present",
"Alignment" = "Alignment MS1/MS2",
"Intensity" = "Intensity is good",
"Noise" = "MS is noisy")),
textInput("text", "Comments:"),
tableOutput("data")
)
)
)
)
plotall <- function(i) {
eic <- eics[[i]]
maybekid <- maybekids[[i]]
fn_ini <- lapply(wd,get_stgs_fn)
lbls <- lapply(fn_ini,function(x) {s <- yaml::yaml.load_file(x);s$prescreen$tag})
dfs <- lapply(file.path(dfdir,eic),function(fn) {
tryCatch(read.csv(fn,stringsAsFactors = F),
error=function(e) {message(paste(e,"; offending file:",fn))})
})
dfs <- lapply(dfs,function(x) data.frame(rt=x$rt/60.,intensity=x$intensity))
## Find existing children.
maybes <- file.path(dfdir,maybekid)
indkids <- which(file.exists(maybes))
kids <- maybes[indkids]
dfs_kids <- lapply(kids,read.csv,stringsAsFactors=F)
dfs_kids <- lapply(dfs_kids,function(x) data.frame(rt=x$retentionTime/60.,intensity= -x$intensity))
## Find max intensities.
w_max <- sapply(dfs,function (x) which.max(x$intensity))
rt_max <- Map(function(df,w) df$rt[[w]],dfs,w_max)
i_max<- Map(function(df,w) df$intensity[[w]],dfs,w_max)
symbs <- LETTERS[1:length(w_max)]
## Find max intensities in children
w_max_kids <- sapply(dfs_kids,function (x) which.max(abs(x$intensity)))
rt_max_kids <- Map(function(df,w) df$rt[[w]],dfs_kids,w_max_kids)
i_max_kids <- Map(function(df,w) df$intensity[[w]],dfs_kids,w_max_kids)
symbs_kids<- letters[indkids]
rt_rng <- range(sapply(dfs,function(x) x$rt))
int_rng <- range(sapply(append(dfs_kids,dfs),function(x) x$intensity))
cols <- RColorBrewer::brewer.pal(n=length(dfs),name=pal)
lgnd <- Map(function(k,v) paste(k,"= ",formatC(v,format="f",digits=rt_digits),sep=''),symbs,rt_max)
layout(matrix(c(1,2,3,3), 2, 2, byrow = TRUE),
widths=c(7,8), heights=c(6,6))
struc_xr <- c(0,100)
struc_yr <- c(0,100)
plot(1,1,type="n",xlab="",ylab="",xlim=struc_xr,ylim=struc_yr,xaxt="n",yaxt="n")
rendersmiles2(osmesi[i],coords=c(struc_xr[1],struc_yr[1],struc_xr[2],struc_yr[2]))
col_eng <- c(0,100)
peak_int <- c(0,100)
plot(1,1,type="n",xlab="",ylab="",xlim=col_eng,ylim=peak_int,xaxt="n",yaxt="n",axes = FALSE)
linfo <- legend("topleft",horiz=T,legend=lbls,col=cols,fill=cols,bty="n",cex=cex)
legend(x=linfo$rect$left,y=linfo$rect$top-0.5*linfo$rect$h,horiz=T,legend=lgnd,fill=cols,bty='n',cex=cex)
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,y=linfo$rect$top-1*linfo$rect$h,horiz=T,legend=lgnd_kids,fill=cols[indkids],bty="n",cex=cex)
plot(1,1,xlab="",ylab="",xlim = rt_rng,ylim = int_rng,type="n")
## Plot eic across the directory set.
for (n in seq(length(dfs))) {
df <- dfs[[n]]
col <- cols[[n]]
lines(df$intensity ~ df$rt,col=col)
}
if (length(dfs_kids) >0) {
for (k in 1:length(indkids)) {
lines(intensity ~ rt,data=dfs_kids[[k]],type="h",col=cols_kids[[k]])
}
}
title(main=paste("ID:",i,"Ion m:",formatC(masses[[i]],digits=m_digits,format="f")),xlab="retention time [min]",ylab="intensity")
for (k in seq(length(w_max))) text(rt_max[[k]],i_max[[k]],labels=symbs[[k]],pos=4,offset=0.5*k)
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)
axis(1)
axis(2)
## RChemMass::renderSMILES.rcdk(smiles[[i]],coords=c(x1,y1,x2,y2))
gc()
}
server <- function(input, output) {
output$plot1 <- renderPlot(
{
i=input$idslider
plotall(i)
}
)
}
shiny::shinyApp(ui = ui, server = server)
}
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment