diff --git a/NAMESPACE b/NAMESPACE
index 436b1377865aff1168a3b7dae55f2fc86dfaa1ea..9d3a356fe3b3604a0823d79f56594f64514861ec 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -11,11 +11,17 @@ export(load_data_input)
export(load_inputs)
export(mk_comp_tab)
export(mk_tol_funcs)
+export(mz_input)
+export(new_rv_state)
+export(new_state)
+export(new_state_fn_conf)
export(prescreen)
export(report)
+export(rt_input)
export(run)
export(run_in_dir)
export(save_plots)
+export(setup_phase)
export(sort_spectra)
export(subset_summary)
import(data.table)
diff --git a/R/api.R b/R/api.R
index 7a933c3f0424d679b9d5fbe45a29341ef4a59e30..97c43df52ee6388946dec38a4578a392b689c992 100644
--- a/R/api.R
+++ b/R/api.R
@@ -13,11 +13,26 @@
## limitations under the License.
+##' @export
+new_state <- function() {
+ m <- new_conf()
+ init_state(m)
+}
+
+##' @export
+new_rv_state <- function() react_v(m=list2rev(new_state()))
+
+##' @export
+new_state_fn_conf <- function(fn_conf) {
+ m <- new_state()
+ m$conf <- read_conf(fn_conf)
+ init_state(m)
+}
+
##' @export
run <- function(fn_conf) {
- conf <- read_conf(fn_conf)
- m <- new_state(conf=conf,
- GUI=F)
+ m <- new_state_fn_conf(fn_conf)
+
dir.create(m$conf$project,
showWarnings = F,
recursive = T)
@@ -27,13 +42,22 @@ run <- function(fn_conf) {
##' @export
-run_in_dir <- function(m) {
+setup_phase <- function(m) {
m <- mk_tol_funcs(m)
m <- load_inputs(m)
m <- concurrency(m)
+ m
+}
+##' @export
+run_in_dir <- function(m) {
+ m <- setup_phase(m)
m <- mk_comp_tab(m)
m <- extr_data(m)
m <- prescreen(m)
+ m <- sort_spectra(m)
+ m <- subset_summary(m)
+ m <- create_plots(m)
+ m <- save_plots(m)
invisible(m)
}
@@ -335,6 +359,7 @@ conf_trans <- function(conf) {
prescreen <- function(m) {
## Top-level auto prescreening function.
+ confpres <- conf_trans_pres(m$conf$prescreen)
## TODO need to fix max spec intensity
gen_ms2_spec_tab <- function(ms) {data.table::rbindlist(lapply(1:nrow(ms), function (nr) {
@@ -373,7 +398,7 @@ prescreen <- function(m) {
}
- m$qa <- create_qa_table(m$extr$ms,m$conf$prescreen)
+ m$qa <- create_qa_table(m$extr$ms,confpres)
mms1 <- assess_ms1(m)
m <- assess_ms2(mms1)
fields <- c("Files","adduct","ID",QA_COLS)
diff --git a/R/mix.R b/R/mix.R
index 9f5ec37ccf049019486ab90d0fa0f69b81470c2e..d757c040f5223ef0cc10edc6d09cc424c5c546d5 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -710,24 +710,17 @@ read_conf <- function(fn) {
}
cf$compound$lists <- fnl
- conf_trans(cf)
+ ## conf_trans(cf)
+ cf
}
-new_conf <- function() EMPTY_CONF
-new_state <- function(conf=NULL,fn_conf="",GUI=F) {
- assert(xor(!is.null(conf),nchar(fn_conf)!=0L),
- msg="Provide either conf, or fn_conf, not both, not none.")
- m <- list()
-
- ## Conf setup
- m$conf <- if (!is.null(conf)) conf else read_conf(fn_conf)
+init_state <- function(m) {
if (is.null(m$conf$debug)) m$conf$debug <- F
m$conf$fn_comp <- file.path(m$conf$project, FN_COMP_TAB)
m$conf$fn_summ <- file.path(m$conf$project, FN_SUMM)
m$extr$fn <- file.path(m$conf$project, "extracted.rds")
- m$GUI <- GUI
m$out$tab <- list()
m$input$tab$mzml <- EMPTY_MZML
lab <- gen_uniq_lab(list(),pref="L")
@@ -736,6 +729,41 @@ new_state <- function(conf=NULL,fn_conf="",GUI=F) {
m
}
+base_conf <- function () {
+ m <- list()
+ m$conf <- list(project=getwd(),
+ compounds=list(lists=list(),
+ sets="",
+ data="",
+ fn_comp="",
+ fn_summ=""),
+ extr=list(fn=""))
+ m
+}
+
+extr_conf <- function(m) {
+ m$conf$tolerance <- list("ms1 coarse"=MS1_ERR_COARSE,
+ "ms1 fine"=MS1_ERR_FINE,
+ "eic"=EIC_ERR,
+ "rt"=RT_EXTR_ERR)
+ m
+}
+
+presc_conf <- function(m) {
+ m$conf$prescreen <- list("ms1_int_thresh"=1e5,
+ "ms2_int_thresh"=2.5e3,
+ "s2n"=3,
+ "ret_time_shift_tol"=0.5)
+ m
+}
+
+
+new_conf <- function() presc_conf(
+ extr_conf(
+ base_conf()))
+
+
+
verify_cmpd_l <- function(dt,fn) {
fields <- colnames(EMPTY_CMPD_LIST)
dtflds <- colnames(dt)
@@ -870,6 +898,8 @@ assess_ms1 <- function(m) {
assess_ms2 <- function(m) {
+ presconf <- conf_trans_pres(m$conf$prescreen)
+
## This function takes a spectral list, looks for the members
## inside the retention time window and returns either the indices
## of those that are, or NA.
@@ -895,7 +925,7 @@ assess_ms2 <- function(m) {
## that the single entry in the sublist is not NA.
m$qa$ms[qa_ms1_exists==T,qa_ms2_exists := .(sapply(spec,function (sl) length(sl)>1 || !is.na(sl[[1]])))]
irows <- which(m$qa$ms$qa_ms1_exists & m$qa$ms$qa_ms2_exists)
- rt_win <- 2 * m$conf$prescreen$ret_time_shift_tol
+ rt_win <- 2 * presconf$ret_time_shift_tol
## List of lists of spec indices where MS2 are within the rt
## window.
@@ -911,7 +941,7 @@ assess_ms2 <- function(m) {
## intensity range.
okind_int_ms2 <- m$qa$ms[irows, ][, .(tmp=mapply(pick_ms2_int,
spec,
- m$conf$prescreen$ms2_int_thresh,
+ presconf$ms2_int_thresh,
ms1_int,
SIMPLIFY=F))]$tmp
diff --git a/R/resources.R b/R/resources.R
index 2038de6fd40ded30ad4870b9d239888a335e620b..34890a378780e7904b6cbe59f37861f94adf4097 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -115,6 +115,7 @@ MS1_SN_FAC <- 3.0
## Shiny objects
NUM_INP_WIDTH="15%"
+NUM_INP_HEIGHT="5%"
@@ -148,22 +149,6 @@ FN_DATA_TAB <- "data-files.csv"
## Default number of concurrent workers
NO_WORKERS <- 2
-EMPTY_CONF <- list(project="",
- compounds=list(lists=list(),
- sets=""),
- data="",
- fn_comp="",
- fn_summ="",
- tolerance=list("ms1 coarse"=MS1_ERR_COARSE,
- "ms1 fine"=MS1_ERR_FINE,
- "eic"=EIC_ERR,
- "rt"=RT_EXTR_ERR),
- prescreen=list("ms1_int_thresh"=1e5,
- "ms2_int_thresh"=2.5e3,
- "s2n"=3,
- "ret_time_shift_tol"=0.5),
- extr=list(fn=""))
-
## Input parameters for prescreening.
CONF_PRES_NUM <- c("ms1_int_thresh","ms2_int_thresh","s2n")
CONF_PRES_TU <- c("ret_time_shift_tol")
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index 7035d4b3f5cf49acc2ad5158458070b8eec88af9..63fbd64a622190fbb894d938676cad21904f162e 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -88,6 +88,44 @@ txt_file_input <- function(inputId,input,fileB,label,volumes,default = "") {
}
+##' @export
+mz_input <- function(input_mz,input_unit,width=NUM_INP_WIDTH,height=NUM_INP_HEIGHT,def_mz=0,def_unit="Da") {
+ style <- "display: inline-block; vertical-align:top; width: "
+ stylel <- "display: inline-block; vertical-align:top;"
+ style=paste0(style,width,"; ")
+ shiny::div(shiny::div(style=stylel,
+ shiny::tags$label("+/-",`for`=input_mz)),
+ shiny::div(style=style,
+ shiny::numericInput(input_mz,
+ label=NULL,
+ value = def_mz)),
+ shiny::div(style=style,
+ shiny::selectInput(input_unit,
+ label=NULL,
+ c("ppm","Da"),
+ selected=def_unit)))
+}
+
+##' @export
+rt_input <- function(input_rt,input_unit,width=NUM_INP_WIDTH,height=NUM_INP_HEIGHT,def_rt=0,def_unit="min") {
+ style="display: inline-block; vertical-align:top; width: "
+ style=paste0(style,width,"; ")
+ stylel <- "display: inline-block; vertical-align:top;"
+ shiny::div(shiny::div(style=stylel,
+ shiny::tags$label("+/-",`for`=input_rt)),
+ shiny::div(style=style,
+ shiny::numericInput(input_rt,
+ label=NULL,
+ value = def_rt)),
+ shiny::div(style=style,
+ shiny::selectInput(input_unit,
+ label=NULL,
+ c("min","s"),
+ selected=def_unit)))
+
+}
+
+
rev2list <- function(rv) {
## Take reactive values structure and convert them to nested
## lists.
@@ -101,14 +139,6 @@ list2rev <- function(lst) {
lst else do.call(react_v,lapply(lst,list2rev))
}
-new_rv_state <- function(project) {
- p <- normalizePath(path=project,winslash = '/')
- nc <- new_conf()
- nc$project <- project
- x <- react_v(m=list2rev(new_state(conf=nc,GUI=T)))
- x
-}
-
mk_roots <- function(wd) local({
addons <- c("project"=normalizePath(wd,winslash = '/'))
def_vol <- function() {