System to synthetise bogus MS spectra completed.

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
 }

tests/testthat/helper-plotting.R

-PLOTTING_DATA <- readRDS(system.file("testdata","plotting-test-data.rds",package="shinyscreen"))
+## PLOTTING_DATA <- readRDS(system.file("testdata","plotting-test-data.rds",package="shinyscreen"))
 

tests/testthat/setup-plotting.R

-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(
+## }
+

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)
 })

tests/testthat/test-plotting.R

+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