Newer
Older
mkUI <- function(idSliderRange,setName,rtRange,tags,QANms) {
names(QANms) <- QANms
tabPanelList <- lapply(tags, function(tag) {
shiny::tabPanel(tag, shiny::checkboxGroupInput(paste("spectProps",tag,sep=""), "Quality Control",
QANms),
shiny::textAreaInput(paste("caption",tag,sep=""), "Comments:", "Insert your comment here..."),
shiny::verbatimTextOutput(paste("value",tag,sep=""))
)})
nvPanel <- do.call(shiny::navlistPanel, tabPanelList)
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
## Prescreening elements
preshead <- shinydashboard::dashboardHeader(title = "Prescreening")
presMenuItem <- shinydashboard::menuItem(text = "The Prescreening",
tabName = "Prescreen",
icon = shiny::icon("dashboard"))
presCompInfo <- shiny::fluidRow(shinydashboard::box(title = "MS Prescreening",
width = 7,
height = "80px",
background = "blue",
""),
shinydashboard::box(title = "Compound ID N°",
width = 5,
height = "80px",
background = "olive",
shiny::textOutput("compoundID")))
presPlotBox <- shinydashboard::box(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 Plots",
icon = shiny::icon("save")))
presCompSelBox <- shinydashboard::box(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))
presQABox <- shinydashboard::box(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",
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
shiny::actionButton("savefiletable",
"Save File Table",
icon = shiny::icon("save")))
presPlotParBox <- 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]))
presPlotWidget <- shiny::fluidRow(presPlotBox,
presCompSelBox,
presQABox,
presPlotParBox)
presTabItem <- shinydashboard::tabItem(tabName = "Prescreen",
shiny::h2("The Prescreen plot"),
presCompInfo,
presPlotWidget)
## Assemble the UI.
ui <- shinydashboard::dashboardPage(skin="black",
shinydashboard::dashboardSidebar(width = 350,
shinydashboard::sidebarMenu(presMenuItem)),
shinydashboard::dashboardBody(shinydashboard::tabItems(presTabItem)))}
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
##' Prescreening using shiny interface.
##'
##' @title Prescreening with Shiny
##' @return Nothing useful.
##' @author Jessy Krier
##' @author Mira Narayanan
##' @author Hiba Mohammed Taha
##' @author Anjana Elapavalore
##' @author Todor Kondić
##' @param prescdf File table data-frame. Columns: Files,ID,wd,tag,set_name ...
##' @param mode RMassBank mode.
##' @param fn_cmpd_l Compound list file name.
##' @param pal ColorBrewer palette.
##' @param cex Size of fonts.
##' @param rt_digits Number of decimal places for the retention time.
##' @param m_digits Number of decimal places for the mass.
##' @export
presc.shiny <-function(prescdf=NULL,mode=NULL,fn_cmpd_l=NULL,pal="Dark2",cex=0.75,rt_digits=2,m_digits=4){
## Helper functions
queryFileTable <- function(df,id) {
df[df$ID %in% id,]
}
updateFileTable <- function(df,id,linput) {
for (tag in names(linput)) {
entries <- names(linput[[tag]])
cond <- (df$ID %in% id) & (df$tag == tag)
df[cond,entries] <- linput[[tag]]
}
df
}
## Constants
MODEMAP=list(pH="MpHp_mass",
mH="MmHm_mass",
blahnh4="MpNH4_mass",
blahna="MpNa_mass")
DEFAULT_RT_RANGE=c(NA,NA)
QANAMES <- c("MS1","MS2","Alignment","AboveNoise")
prescdf$tag <- as.character(prescdf$tag)
tags <- levels(factor(prescdf$tag))
wd <- prescdf$wd[match(tags,prescdf$tag)]
wd1 <- wd[[1]]
cmpd_l_df <- read.csv(file=fn_cmpd_l,stringsAsFactors = F,comment.char='')
preID <- as.integer(levels(factor(prescdf$ID)))
selID <- which(cmpd_l_df$ID %in% preID)
osmesi <- cmpd_l_df$SMILES[selID]
no_cmpds <- length(preID)
# reconf(wd1)
masses <- lapply(osmesi,function (smile) {
#osmesi <- tryCatch(RMassBank::findSmiles(i), error = function(e) NA)
zz <- RChemMass::getSuspectFormulaMass(smile)
zz[[MODEMAP[[mode]]]]
})
names(osmesi) <- as.character(preID)
names(masses) <- as.character(preID)
## Get the basenames of eic files.
eics <- list.files(path=wd[[1]],patt=".*eic.csv")
eicsPref <- sapply(strsplit(eics,split="\\."),function(x) x[[1]])
eicsID <- as.integer(eicsPref)
maybekids <- sapply(eicsPref,function(x) {paste(x,'.kids.csv',sep='')})
names(eics) <- eicsID
names(maybekids) <- eicsID
plot_id <- function (i,rtrange=NULL,log=rv$yaxis) plot_id_aux(i=as.character(i),wd=wd,eics=eics,maybekids=maybekids,mass=masses[[as.character(i)]],smile=osmesi[[as.character(i)]],tags=tags,log=log,rtrange=rtrange,cex=cex,pal=pal,rt_digits=rt_digits,m_digits=m_digits,fTab=prescdf)
spectProps <- sapply(tags,function (tag) paste("spectProps",tag,sep=""))
idSliderRange <- c(1,length(preID))
ui <- mkUI(idSliderRange=idSliderRange,setName=prescdf$set_name,rtRange=DEFAULT_RT_RANGE,tags=tags,QANms=QANAMES)
getCheckboxValues <- function(tag,input) {
chkbox <- input[[spectProps[[tag]]]]
q <- sapply(QANAMES,function (qn) if (qn %in% chkbox) T else F)
names(q) <- QANAMES
q
}
server <- function(input, output, session) {
rv <- shiny::reactiveValues(prescList=list(),
prescdf=prescdf,
spectProps=spectProps,
tags=tags,
default_range=DEFAULT_RT_RANGE,
no_cmpds=no_cmpds)
output$plot1 <- renderPlot(
{
i=preID[[input$idslider]]
rtrange <- c(input$min_val,input$max_val)
plot_id(i,rtrange=rtrange, log=input$yaxis)
# intParameter <- c(input$nice, input$steps)
})
output$value <- renderText(
{
input$caption
})
output$compoundID <- renderText(
{
preID[[input$idslider]]
})
shiny::observeEvent(input$saveplot,
{
i=preID[[input$idslider]]
pfn <-input$plotname
if (is.na(pfn)) pfn <- "plotCpdID_%i.pdf"
fn <- sprintf(pfn,i)
rtrange <- c(input$min_val,input$max_val)
pdf(file=fn, width=12, height=8)
plot_id(i,rtrange=rtrange, log=input$yaxis)
dev.off()
})
shiny::observeEvent(input$saveallplots,
{
i=preID[[input$idslider]]
pfn <-input$plotname
if (is.na(pfn)) pfn <- "plotall.pdf"
fn <- sprintf(pfn,i)
pdf(file=fn, width=12, height=8)
for (i in preID) {
plot_id(i,log=input$yaxis)
message("Compound ID ",i," done.")
}
dev.off()
})
shiny::observeEvent(input$submitQA,{
res <- lapply(rv$tags,getCheckboxValues,input)
names(res) <- rv$tags
rv$prescdf <- updateFileTable(df=rv$prescdf,id=preID[[input$idslider]],linput=res)
})
shiny::observe({
i <- preID[[input$idslider]]
sdf <- queryFileTable(df=rv$prescdf,id=i)
for (t in sdf$tag) {
sprop <- rv$spectProps[[t]]
sel <- as.logical(sdf[sdf$tag %in% t,QANAMES])
choices <- QANAMES[sel]
names(choices) <- QANAMES[sel]
shiny::updateCheckboxGroupInput(session = session,inputId = sprop,selected=choices)
}
})
shiny::observeEvent(input$savefiletable,
{
write.csv(file=input$fn_ftable,x=rv$prescdf,row.names = F)
})
session$onSessionEnded(function() {
stopApp()
})
}
shiny::shinyApp(ui = ui, server = server)
}
mkUI2 <- function() {
browseFile <- function(title,
buttonName,
txtName,
txtTxt="",
icon="file",
confImport <- shinydashboard::box(title="Import",
shiny::h5("There are two tables that need to be supplied before prescreening starts. One is the compound list, its format being the same like the one for the RMassBank (fields: ID,Name,SMILES,RT,CAS,mz,Level). Another is the compound set table (fields: ID,set). Once those tables are imported, they can further be modified as copies inside the project dir. Shinyscreen will never modify any initial (meta)data. If set field of the compound set table is NA, then that file is in a set of its own."),
shiny::textInput("impCmpListInp",
"Compound set table.",
value=""),
shiny::textInput("impGenRMBInp",
"RMassBank settings.",
shinyFiles::shinyFilesButton("impCmpListB",
label="Import compound list.",
title="",
icon=shiny::icon("file"),
shinyFiles::shinyFilesButton("impSetIdB",
label="Import compound set table.",
title="",
icon=shiny::icon("file"),
multiple=T),
shinyFiles::shinyFilesButton("impGenRMBB",
label="Import RMassBank settings.",
title="",
icon=shiny::icon("file"),
multiple=F),
width=NULL)
confmzMLTags <- shinydashboard::box(title="Sets and Tags",
shiny::h5("Shinyscreen uses two properties, tags and sets, to categorise mzML data. Tags are properties of individual files. For example, if a single file represents a collection of spectra acquired at a specific collision energy, that energy could be used as a tag. Tags are used to differentiate the spectra in a chromatogram. Sets are collections of tagged files and are read from the compound set table. Each set is going to be screened for a designated collection of masses."),
shiny::textInput("tagPropInp",
"What is a tag? (example: collision energy; can be left empty.)",
value=""),
shiny::textInput("tagsInp",
"Comma-delimited list of tag types",
value=""),
width=NULL)
confState <- shinydashboard::box(title="Configuration state",
shiny::h5("Saves and restores current configuration."),
shinyFiles::shinySaveButton("saveConfB",
"Save configuration",
title="Save",
filename = "conf-state.rds",
"rds"),
shinyFiles::shinyFilesButton("restoreConfB",
label="Restore configuration",
multiple=F,
title="Restore"),
## confFileTab<-shinydashboard::box(title="File table generation settings",
## shinyFiles::shinySaveButton("confFileTabB",
## "Basic file table.",
## "Basic file table.",
## filename = FN_FTAB_BASE,
## "csv"),
## width=NULL)
confPP<-shinydashboard::box(title="Preprocessing settings",
shiny::textInput("confFileTabBase",
"Basic file table.",
value=FN_FTAB_BASE),
shiny::textInput("confFileTabProcInp",
"Preprocessed file table.",
value=FN_FTAB_PP),
shiny::textInput("confResFileTab",
"Resulting file table.",
value=FN_FTAB),
width=NULL)
confmzMLtab <-shinydashboard::box(title="mzML file table",
shiny::h5("Use this file table to assign adduct modes and tags to the data files."),
shinyFiles::shinyFilesButton("mzMLB",
label="Select mzML files",
title="Select mzML files",
icon=shiny::icon("files"),
multiple=T),
rhandsontable::rHandsontableOutput("mzMLtabCtrl"),
width=NULL)
confLayout <- shiny::fluidRow(shiny::column(confImport,
confState,
width=4),
shiny::column(width=8,
confTab <- shinydashboard::tabItem(tabName="config",
confLayout)
## ***** Compound List Tab *****
cmpListBox<-shinydashboard::box(title="Compound list",
rhandsontable::rHandsontableOutput("cmpListCtrl"),
width=NULL)
cmpListState <- shinydashboard::box(title="Compound list state",
shinyFiles::shinySaveButton("saveCmpListB",
"Save",
title="Save",
filename = "compounds.csv",
"csv"),
shinyFiles::shinyFilesButton("restoreCmpListB",
label="Restore",
multiple=F,
title="Restore"),
width=NULL)
cmpListLayout <- shiny::fluidRow(shiny::column(cmpListState,
cmpListBox,
width = 12))
cmpListTab <- shinydashboard::tabItem(tabName="compList",
shiny::h5("This is an editable view of the compound list."),
## ***** Sets of compounds *****
setIdBox<-shinydashboard::box(title="Compound sets",
width = NULL)
setIdBoxState<-shinydashboard::box(title="Compound list state",
shinyFiles::shinySaveButton("saveSetIdB",
"Save",
title="Save",
filename = "compound_sets.csv",
"csv"),
shinyFiles::shinyFilesButton("restoreSetIdB",
label="Restore",
multiple=F,
title="Restore"),
width=NULL)
setIdLayout<-shiny::fluidRow(shiny::column(setIdBoxState,
setIdBox,
width = 12))
setIdTab<-shinydashboard::tabItem(tabName="setId",
shiny::h5("This is an editable view of the id/set list."),
setIdLayout)
## ***** Generate Prescreen Data *****
## genBox<-shinydashboard::box(title="Produce file table",
## shiny::actionButton(inputId="genRunB",
## label="Run!",
## icon=shiny::icon("bomb")),
## ,
## width=NULL)
genBoxParam1<-shinydashboard::box(title="Parameters of the run",
shiny::textInput("genNoProc",
label="Number of processes.",
value=1),
shiny::textInput("ppmLimFine",
label="ppm limit fine",
value=10),
shiny::textInput("eicLim",
label="EIC limit.",
value=1e-3),
shiny::textInput("intTresh",
label="Intensity threshold.",
value=1e5),
shiny::textInput("noiseFac",
label="Signal-to-noise ratio.",
value=3),
shiny::textInput("rtDelta",
label="Retention time Δ",
value=0.5),
width=NULL)
genBoxParam2<-shinydashboard::box(title=NULL,
shiny::selectInput("genSetSelInp",
label="Select set(s).",
choices="",
multiple=T),
shiny::actionButton(inputId="genRunB",
label="Run!",
icon=shiny::icon("bomb")),
width=NULL)
genBoxProcessed<-shinydashboard::box(title="Processed sets",
shiny::actionButton(inputId="genFileTabB",
label="Generate file table.",
icon=shiny::icon("save")),
shiny::actionButton(inputId="genRunPPB",
label="Preprocess!",
icon=shiny::icon("bomb")),
rhandsontable::rHandsontableOutput("genTabProcCtrl"),
width=NULL)
genTab<-shinydashboard::tabItem(tabName = "gen",
shiny::h5("Prepare for prescreening."),
shiny::fluidRow(shiny::column(genBoxProcessed,
shiny::fluidRow(shiny::column(genBoxParam1,width=4)),
shiny::fluidRow(shiny::column(genBoxParam2,width=4)))
## ***** Prescreening *****
presTab <- shinydashboard::tabItem(tabName="prescreen")
headerText <- "Shinyscreen"
confSideItem <- shinydashboard::menuItem(text="Config",
tabName="config",
compListSideItem <- shinydashboard::menuItem(text="Compound list",
tabName="compList",
setIdSideItem <- shinydashboard::menuItem(text="Compound sets",
tabName="setId",
icon=shiny::icon("table"))
genSideItem <- shinydashboard::menuItem(text="Generate prescreen data",
tabName="gen",
icon=shiny::icon("cogs"))
presSideItem <- shinydashboard::menuItem(text="Prescreening",
tabName="prescreen",
header <- shinydashboard::dashboardHeader(title=headerText)
sidebar <- shinydashboard::dashboardSidebar(shinydashboard::sidebarMenu(confSideItem,
compListSideItem,
body <- shinydashboard::dashboardBody(shinydashboard::tabItems(confTab,
shinydashboard::dashboardPage(header,
sidebar,
body)}
##' @export
shinyScreenApp <- function(projDir=getwd()) {
modeLvl<- c("pH","pNa","pM",
"mH","mFA")
mk_mzMLtab<-function() {
modeLvl<- c("pH","pNa","pM",
"mH","mFA")
res<-data.frame(Files=character(),
mode=factor(levels=modeLvl),
stringsAsFactors=F)
res
}
mk_cmpList<-function() {
data.frame(ID=integer(),
Name=character(),
SMILES=character(),
RT=double(),
CAS=character(),
stringsAsFactors = F)
}
mk_setId<-function() {
data.frame(ID=integer(),
set=character())}
modeLvl<- c("select","pH","pNa","pM",
"mH","mFA")
lSet<-levels(ft$set)
lTag<-levels(ft$tag)
newRow<-data.frame(Files=fn,
mode=factor(modeLvl[[1]],levels=modeLvl),
set=if (length(lSet) > 0) factor(lSet[[1]],levels=lSet) else factor("unspecified"),
tag=if (length(lTag) > 0) factor(lTag[[1]],levels=lTag) else factor("unspecified"),
stringsAsFactors = F)
levels(newRow$mode)<-modeLvl
res<-rbind(ft,newRow,
stringsAsFactors = F,
make.row.names = F)
levels(res$mode)<-modeLvl
readCmpList<-function(fn) {
read.csv(file=fn,
header=T,
stringsAsFactors = F,
comment.char = '')
}
readSetId<-function(fn) {
read.csv(file=fn,
header=T,
stringsAsFactors = T,
comment.char = '',
na.strings = c("","NA"))
}
server <- function(input,output,session) {
rvConf <- shiny::reactiveValues(mzMLtab=mk_mzMLtab(),
tags=list(),
sets=list(),
tagProp="",
setProp="",
rvCmpList<- shiny::reactiveValues(df=mk_cmpList())
rvSetId<- shiny::reactiveValues(df=mk_setId())
## ***** shinyFiles observers *****
wdroot<-c(wd=projDir)
shinyFiles::shinyFileChoose(input, 'impCmpListB',roots=volumes)
shinyFiles::shinyFileChoose(input, 'impSetIdB',roots=volumes)
shinyFiles::shinyFileChoose(input, 'impGenRMBB',roots=volumes)
shinyFiles::shinyFileSave(input, 'saveConfB',roots=wdroot)
shinyFiles::shinyFileChoose(input, 'restoreConfB',roots=wdroot)
shinyFiles::shinyFileChoose(input, 'mzMLB',roots=volumes)
shinyFiles::shinyFileSave(input, 'saveCmpListB',roots=wdroot)
shinyFiles::shinyFileChoose(input, 'restoreCmpListB',roots=projDir)
shinyFiles::shinyFileSave(input, 'saveSetIdB',roots=wdroot)
shinyFiles::shinyFileChoose(input, 'restoreSetIdB',roots=wdroot)
## ***** reactive function definitions *****
getTags<-shiny::reactive({
if (length(input$tagsInp)>0 && !is.na(input$tagsInp)) unlist(strsplit(input$tagsInp, ",")) else list()
})
getSets<-shiny::reactive({
update_tags_mzMLtab<-shiny::reactive({
tags<-getTags()
tagCol<-rvConf$mzMLtab$tag
if (length(levels(tagCol))==0) rvConf$mzMLtab$tag<-factor(tagCol)
rvConf$mzMLtab$tag<-factor(tagCol,levels=tags)
update_sets_mzMLtab<-shiny::reactive({
sets<-getSets()
setCol<-rvConf$mzMLtab$set
if (length(levels(setCol))==0) rvConf$mzMLtab$set<-factor(setCol)
rvConf$mzMLtab$set<-factor(setCol,levels=sets)
fn<-shinyFiles::parseSavePath(root=c(wd=rvConf$projDir),input$saveConfB)[["datapath"]]
sav<-list()
sav<-list(rvConf=list(),
input=list())
shiny::isolate(for (nm in names(rvConf)) {
sav$rvConf[[nm]]<-rvConf[[nm]]
})
sav$input$tagsInp<-input$tagsInp
sav$input$setsInp<-input$setsInp
sav$input$impCmpListInp<-input$impCmpListInp
sav$input$impSetIdInp<-input$impSetIdInp
sav$input$impGenRMBInp<-input$impGenRMBInp
saveRDS(object=sav,file=fn)
}
})
restoreConf<-reactive({
input$restoreConfB
fnobj<-shinyFiles::parseFilePaths(root=c(wd=rvConf$projDir),input$restoreConfB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
message("Restoring config from",fn)
sav<-readRDS(fn)
for (nm in names(sav$rvConf)) {
rvConf[[nm]]<-sav$rvConf[[nm]]
}
#FIXME: remove this, once local saves/restores supported
rvConf$freshCmpListInp<-T
rvConf$freshSetIdInp<-T
shiny::updateTextInput(session=session,
inputId="tagsInp",
value=sav$input$tagsInp)
shiny::updateTextInput(session=session,
inputId="impCmpListInp",
value=sav$input$impCmpListInp)
shiny::updateTextInput(session=session,
inputId="impGenRMBInp",
value=sav$input$impGenRMBInp)
shiny::updateTextInput(session=session,
inputId="impSetIdInp",
value=sav$input$impSetIdInp)
shiny::updateTextInput(session=session,
inputId="confFileTabBase",
value=sav$input$confFileTabBase)
shiny::updateTextInput(session=session,
inputId="confFileTabProcInp",
value=sav$input$confFileTabProcInp)
shiny::updateTextInput(session=session,
inputId="confResFileTab",
value=sav$input$confResFileTab)
getCmpListdf<-shiny::reactive({rvCmpList$df})
importCmpListdf<-shiny::reactive({
impCmpFn<-input$impCmpListInp
if (length(impCmpFn)>0 && !is.na(impCmpFn)) {
message("Importing compound list from ",impCmpFn)
rvConf$impCmpListFn<-impCmpFn
rvConf$freshCmpListImp<-T
rvCmpList$df<-readCmpList(rvConf$impCmpListFn)
}
})
impSetIdFn<-input$impSetIdInp
if (length(impSetIdFn)>0 && !is.na(impSetIdFn)) {
message("Importing setid table from ",impSetIdFn)
rvConf$impSetIdFn<-impSetIdFn
rvConf$freshSetIdImp<-T
rvSetId$df<-readSetId(rvConf$impSetIdFn)
}
})
shiny::observe({
input$mzMLB
fchoice<-shinyFiles::parseFilePaths(root=volumes,input$mzMLB)
paths<-fchoice[["datapath"]]
isolate({
for (pt in paths) {
rvConf$mzMLtab<-extd_mzMLtab(rvConf$mzMLtab,pt)
}
shiny::observeEvent(input$mzMLtabCtrl,{
input$cmpListCtrl
input$setIdTabCtrl
shiny::isolate({rvConf$mzMLtab<-rhandsontable::hot_to_r(input$mzMLtabCtrl)})
})
shiny::observeEvent(input$cmpListCtrl,{
shiny::isolate({rvCmpList$df<-rhandsontable::hot_to_r(input$cmpListCtrl)})
})
shiny::observeEvent(input$setIdTabCtrl,{
df<-rhandsontable::hot_to_r(input$setIdTabCtrl)
rvSetId$df<-df
shiny::updateSelectInput(session=session,
inputId="genSetSelInp",
choices=levels(df$set))})
shiny::observeEvent(input$restoreConfB,{
message("Restore event observed.")
restoreConf()
})
shiny::observeEvent(input$saveConfB,{
saveConf()
})
## shiny::observeEvent(input$confFileTabBase, {
## fn<-input$confFileTabBase
## if (length(fn)>0 && !is.na(fn)) {
## rvConf$FileTabFn<-fn
## }
## })
shiny::observeEvent(input$genFileTabB,{
if (length(fn)>0 && !is.na(fn)) {
message("Saving file table to",fn)
files<-adornmzMLTab(rhandsontable::hot_to_r(input$mzMLtabCtrl),projDir=rvConf$projDir)
setId<-rhandsontable::hot_to_r(input$setIdTabCtrl)
genSuprFileTbl(files,setId,destFn=fn)
})
shiny::observeEvent(input$genRunB,{
FnRMB<-input$impGenRMBInp
nProc<-as.integer(input$genNoProc)
fnTab<-rvConf$FileTabFn
sets<-input$genSetSelInp
message("Selected sets:")
message(str(sets))
message("Number of processes:",nProc)
message("RMassBank settings file:",FnRMB)
message("File table:",fnTab)
if (length(fnTab)>0) {
## fTab<-read.csv(file=fnTab,
## row.names=F,
## heander=T,
## comment.char='',
## na.strings=c("","NA"),
## stringsAsFactors=F)
## mask<-fTab$set %in% sets
## fTab<-fTab[mask,]
for (s in sets) {
fnCmpdList<-input$impCmpListInp
fnStgs<-input$impGenRMBInp
intTresh<-as.numeric(input$intTresh)
noiseFac<-as.numeric(input$noiseFac)
rtDelta<-as.numeric(input$rtDelta)
ppmLimFine<-as.numeric(input$ppmLimFine)
dest<-rvConf$projDir
eicLim<-as.numeric(input$eicLim)
gc()
gen(fnFileTab=fnTab,
fnCmpdList=fnCmpdList,
fnStgs=fnStgs,
dest=dest,
proc=nProc,
intTresh=intTresh,
noiseFac=noiseFac,
rtDelta=rtDelta,
ppmLimFine=ppmLimFine,
eicLim=eicLim)
output$mzMLtabCtrl <- rhandsontable::renderRHandsontable({
rvConf$mzMLtab
update_tags_mzMLtab()
update_sets_mzMLtab()
if (nrow(rvConf$mzMLtab) !=0) rhandsontable::rhandsontable(rvConf$mzMLtab,stretchH="all") else NULL
})
shiny::observeEvent(input$impSetIdB,{
fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impSetIdB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
shiny::updateTextInput(session=session,
inputId="impSetIdInp",
value=fn)
}})
shiny::observeEvent(input$impCmpListB,{
fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impCmpListB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
shiny::updateTextInput(session=session,
inputId="impCmpListInp",
value=fn)
}})
shiny::observeEvent(input$impGenRMBB,{
fnobj<-shinyFiles::parseFilePaths(roots=volumes,input$impGenRMBB)
fn<-fnobj[["datapath"]]
if (length(fn)>0 && !is.na(fn)) {
shiny::updateTextInput(session=session,
inputId="impGenRMBInp",
value=fn)
}})
shiny::observeEvent(input$genRunPPB,{
shiny::isolate({
sets<-getSets()
cdf<-if (!is.null(input$cmpListCtrl)) rhandsontable::hot_to_r(input$cmpListCtrl) else NULL})
nr<-nrow(cdf)
if (!is.null(nr)) {
if (is.na(nr)) nr<-0
} else nr<-0
if (length(sets)>0 && nr>0) {
doneSets<-sets[sapply(sets,isGenDone)]
if (length(doneSets)>0) {
fnFullTab<-input$confFileTabProcInp
fnBaseTab<-input$confFileTabBase
fnOpen<-""
fnOpen<-if (file.exists(fnFullTab)) fnFullTab else fnBaseTab
fullFTab<-read.csv(file=fnOpen,
comment.char = '',
stringsAsFactors = F)
doneFTab<-fullFTab[fullFTab$set %in% doneSets,]
if (nrow(doneFTab)>0) {
fnTmp<-ppInpFt()
write.csv(file=fnTmp,
x=doneFTab,
row.names=F)
message("fnTmp: ",fnTmp)
cmpdL<-rhandsontable::hot_to_r(input$cmpListCtrl)
maxId<-do.call(max,sapply(doneSets,idsFromFiles))
message("maxId: ",maxId)
intTresh<-as.numeric(input$intTresh)
noiseFac<-as.numeric(input$noiseFac)
rtDelta<-as.numeric(input$rtDelta)
## dr<-file.path(dirname(fnCand),sets)
preProc(fnFileTab=fnTmp,
lCmpdList=maxId,
fnDest=fnTmp,
intTresh=intTresh,
noiseFac=noiseFac,
rtDelta=rtDelta)
comment.char = '',
stringsAsFactors = F)
extNms<-names(ppFnTab)
basNms<-names(fullFTab)
diffNms<-setdiff(extNms,basNms)
nrf<-nrow(fullFTab)
for (nm in diffNms) {
z<-logical(length=nrf)
z<-T
fullFTab[[nm]]<-z
}
fullFTab[fullFTab$set %in% doneSets,]<-ppFnTab
write.csv(file=fnFullTab,
x=fullFTab,
row.names=F)
}
}
}
input$impGenRMBInp
input$impSetIdInp
input$impCmpListInp
output$cmpListCtrl <- rhandsontable::renderRHandsontable({
importCmpListdf()
if (rvConf$freshCmpListImp) {
shiny::isolate({
rvConf$freshCmpListImp<-F