diff --git a/R/data-model.R b/R/data-model.R
index 973b9223caf1fb5268978e0f5c71d664391b5b0d..04ce025cae08488e1718359b63254bc2e3e8916b 100644
--- a/R/data-model.R
+++ b/R/data-model.R
@@ -118,7 +118,7 @@ empty_cgram_ms1 <- function(n=0L) {
empty_cgram_ms2 <- function(n=0L) {
r = data.table(precid=integer(n),
ce=numeric(n),
- scan=integer(n),
+ scan=character(n),
idx=integer(n),
rt=numeric(n),
intensity=numeric(n))
@@ -128,11 +128,11 @@ empty_cgram_ms2 <- function(n=0L) {
}
-empty_spectra_table <- function() {
- r = data.table(precid=integer(0),
- scan=character(0),
- mz=numeric(0),
- intensity=numeric(0))
+empty_spectra_table <- function(n=0L) {
+ r = data.table(precid=integer(n),
+ scan=character(n),
+ mz=numeric(n),
+ intensity=numeric(n))
setkey(r,precid,scan)
r
}
diff --git a/inst/testdata/plotting-test-data.rds b/inst/testdata/plotting-test-data.rds
deleted file mode 100644
index 6a7745a4655b5663e348687366499a25a1ad0147..0000000000000000000000000000000000000000
Binary files a/inst/testdata/plotting-test-data.rds and /dev/null differ
diff --git a/tests/testthat/helper-plotting.R b/tests/testthat/helper-plotting.R
index fe15a08dd74147a4050a8eed68a2f6f8cc308115..87665e1e0da2ac9e4c3b1d86315d0c15ef8bb1d7 100644
--- a/tests/testthat/helper-plotting.R
+++ b/tests/testthat/helper-plotting.R
@@ -1,2 +1,2 @@
-PLOTTING_DATA <- readRDS(system.file("testdata","plotting-test-data.rds",package="shinyscreen"))
+## PLOTTING_DATA <- readRDS(system.file("testdata","plotting-test-data.rds",package="shinyscreen"))
diff --git a/tests/testthat/setup-plotting.R b/tests/testthat/setup-plotting.R
index 6debe7807fa960185fcb09e8b16558800e7c7202..db9b6ea87138d888e679f7ab56c9777ad85ec8ad 100644
--- a/tests/testthat/setup-plotting.R
+++ b/tests/testthat/setup-plotting.R
@@ -1 +1,125 @@
-PLOTTINGDATA <- system.file("testdata","plotting-test-data.rds")
+
+
+
+PLOTTING_STATE_DB = readRDS(system.file(package="shinyscreen","testdata","plotting-state-db.rds"))
+
+
+synthetise_cgm_ms1 <- function(n,fac,shift) {
+ dt = data.table(rt=numeric(n),intensity=numeric(n))
+ dt[1L:n,rt:=seq(length.out=n)]
+ rt0 = dt[.N/2L + shift,rt]
+ dt[,intensity:=fac*exp(-((rt - rt0)/2.)**2)]
+}
+
+synthetise_cgm_ms2 <- function(cgm1,shift) {
+ dt = copy(cgm1)
+ m = dt[,max(intensity)]
+ n0 = dt[,.N%/%2L] + shift
+ dt[,intensity:=NA_real_]
+ dt[n0-1L,intensity:=0.05*m]
+ dt[n0,intensity:=0.1*m]
+ dt[n0+1L,intensity:=0.07*m]
+ dt
+}
+
+
+synthetise_spectra <- function(n_mz,precursors,cgm2) {
+
+ do_int <- function(n_mz,i) {
+ things = runif(n_mz - 1L,0.5*i,0.9*i)
+ c(things,i)
+ }
+ do_mass <- function(n_mz,mz) {
+ c(runif(n_mz-1L,0.1*mz,0.7*mz),mz)
+ }
+ cgm2[precursors,on=.(precid),
+ .(mz=do_mass(n_mz,i.mz),
+ intensity=do_int(n_mz,intensity[[1]]),
+ scan=scan[[1]]),
+ by=.EACHI]
+
+}
+
+synthetise_pseudo_state_db <- function(db) {
+
+
+ ## Fix input parameters.
+ set.seed(22) # Random generator seed for reproducible results.
+ n_time = 11L
+ n_mz = 3L
+ n_precid = length(db$precursors[,unique(precid)])
+ n_cgm = n_time * n_precid
+ n_spectra = n_time * n_precid * n_mz
+
+ shifts = sample(c(-1L,0L,1L),size=n_precid,replace=T)
+ facs = runif(n_precid,min=0.5)*1.e8
+ inp = data.table(precid=db$precursors[,unique(precid)],
+ fac=facs,
+ shift=shifts)
+ setkey(inp,precid)
+
+
+
+
+ extr = list()
+ extr$cgm$ms1 = empty_cgram_ms1(n_cgm)
+ extr$cgm$ms2 = empty_cgram_ms2(n_cgm)
+ extr$spectra = empty_spectra_table(n_spectra)
+ uprec = db$precursors[,unique(.SD),.SDcols=c("file","tag","precid")]
+ uprec[,{
+ f=file
+ for (i in seq(length.out=length(precid))) {
+ b=(.GRP-1L)*length(precid)*n_time + (i-1L)*n_time + 1L
+ e=b+n_time - 1L
+ pp = precid[[i]]
+ cx=(.GRP-1L)*length(precid) + i
+
+ faci = inp[precid==pp,fac]
+ shifti = inp[precid==pp,shift]
+ ri = synthetise_cgm_ms1(n=n_time,
+ fac=faci,
+ shift=shifti)
+
+ ri2 = synthetise_cgm_ms2(ri,
+ shift=shifti)
+
+ extr$cgm$ms1[b:e,
+ `:=`(precid=pp,
+ cgmidx=cx,
+ file=f,
+ rt=ri[,rt],
+ intensity=ri[,intensity])]
+
+ scans = paste0("F1.S",formatC(b:e,width=6,flag="0"))
+ extr$cgm$ms2[b:e,
+ `:=`(precid=pp,
+ ce=50,
+ scan=scans,
+ idx=b:e,
+ rt=ri2[,rt],
+ intensity=ri2[,intensity])]
+
+
+
+
+ }
+
+ },
+ by=c("file","tag")]
+ extr$cgm$ms2 = extr$cgm$ms2[!is.na(intensity)]
+ db$extr = extr
+ db$extr$spectra = synthetise_spectra(n_mz,db$precursors,db$extr$cgm$ms2)
+
+ set.seed(NULL)
+
+ browser()
+ 1+1
+ db
+
+}
+
+## synthetise_eic_ms1 <- function(precursors) {
+## ## N =
+## dt = empty_cgram_ms1(
+## }
+
diff --git a/tests/testthat/test-integration.R b/tests/testthat/test-integration.R
index 7c0a667602ba4052725bec275f4af2dc84e1b0a6..3b46dc0ffb0c950440c359dd06e5b26959a0160c 100644
--- a/tests/testthat/test-integration.R
+++ b/tests/testthat/test-integration.R
@@ -13,6 +13,5 @@ test_that("Extraction returns what is needed.",{
m = run(envopts=eo,m=m,phase="extract")
m = run(envopts=eo,m=m,phase="prescreen")
- browser()
expect_true(1==1)
})
diff --git a/tests/testthat/test-plotting.R b/tests/testthat/test-plotting.R
index 1f33bce0ee3ca62ede34c3a04563a3f8cb5ba9f4..bfcf5a3c1af798d510422306f79cd1cee02a7cde 100644
--- a/tests/testthat/test-plotting.R
+++ b/tests/testthat/test-plotting.R
@@ -1,3 +1,10 @@
+test_that("get_data_from_key",{
+
+ s = synthetise_pseudo_state_db(PLOTTING_STATE_DB)
+ expect_identical(1L,1L)
+})
+
+
## test_that("make_eic_ms1_plot",{
## ms1 <- PLOTTING_DATA$ms1