Cleaned up make_eic_ms1_plot and related functions.

R/plotting.R

@@ -285,27 +285,25 @@ get_data_4_eic_ms1 <- function(db,extr_ms1,summ_rows,kvals,labs) {
     keys = names(kvals)
     actual_key = intersect(keys,names(extr_ms1))
     actual_kvals = kvals[actual_key]
-    browser()
+
     ## Subset extr_ms1 by the actual key.
     tab = get_data_from_key(db=db,
                             tab=extr_ms1,
                             kvals=kvals,
-                            outcols = c("mz","rt","intensity"))
+                            outcols = c("catid","mz","rt","intensity"))
+
+
 
-    ## Group the plot data per label group (ie tags, or adducts, or
-    ## both).
-    xlxx = intersect(labs,names(extr_ms1))
-    xlxx = as.character(xlxx)
-    pdata = tab[,.(rt,intensity),by=xlxx]
+    meta = db$cat[tab[,.(catid=unique(catid))],on=.(catid),.SD,by=.EACHI,.SDcols=labs]
 
+    ## Attach catid information.
+    tab = meta[tab,on=.(catid),nomatch=NULL]
+    pdata = tab[,.(rt,intensity),by=labs]
 
-    ## TODO: FIXME: This fails because summ_rows sux wrt calcing of ms1_rt for labels. #Now, add the RTs in.
-    ## pdata[summ_rows,ms1_rt:=signif(i.ms1_rt,5),on=xlxx]
+    text_labels = labs
+    pdata = eval(bquote(pdata[,label:=make_line_label(..(lapply(text_labels,as.symbol))),by=text_labels],splice=T))
+    setkeyv(pdata,cols=unique(as.character(text_labels)))
 
-    ## Create labels.
-    ## xlxx <- unique(c(xlxx,"ms1_rt"))
-    pdata = eval(bquote(pdata[,label:=make_line_label(..(lapply(xlxx,as.symbol))),by=xlxx],splice=T))
-    setkeyv(pdata,cols=unique(as.character(xlxx),"rt"))
     pdata
 }
 
@@ -354,7 +352,6 @@ make_eic_ms1_plot <- function(db,extr_ms1,summ,kvals,labs,axis="linear",rt_range
     ## plots is wrong. Horrible and wrong. Will remove those labels
     ## until we fix.
     summ_rows = narrow_summ(db=db,summ,kvals,labs,"mz","ms1_rt","ms1_int","Name","SMILES","qa_ms1_exists","scan","ms2_sel")
-    browser()
     rows_key = union(data.table::key(summ_rows),labs)
     summ_rows$sel_ms1_rt=NA_real_
     summ_rows[ms2_sel==T,sel_ms1_rt:=ms1_rt[which.max(ms1_int)],by=rows_key]

tests/testthat/_snaps/plotting.md

@@ -3,16 +3,16 @@
     Code
       ns
     Output
-         set ID set ID adduct tag       mz ms1_rt  ms1_int      Name
-      1: AAs  4 AAs  4 [M+H]+  AA 120.0655      4 70481520 Threonine
-      2: AAs  4 AAs  4 [M+H]+  AA 120.0655      4 70481520 Threonine
-      3: AAs  4 AAs  4 [M+H]+  AA 120.0655      4 70481520 Threonine
-      4: AAs  4 AAs  4 [M+H]+  KO 120.0655      4 80851056 Threonine
-      5: AAs  4 AAs  4 [M+H]+  KO 120.0655      4 80851056 Threonine
-      6: AAs  4 AAs  4 [M+H]+  KO 120.0655      4 80851056 Threonine
-      7: AAs  4 AAs  4 [M+H]+  WT 120.0655      5 68987250 Threonine
-      8: AAs  4 AAs  4 [M+H]+  WT 120.0655      5 68987250 Threonine
-      9: AAs  4 AAs  4 [M+H]+  WT 120.0655      5 68987250 Threonine
+         set ID precid adduct tag       mz ms1_rt  ms1_int      Name
+      1: AAs  4      6 [M+H]+  AA 120.0655      4 70481520 Threonine
+      2: AAs  4      6 [M+H]+  AA 120.0655      4 70481520 Threonine
+      3: AAs  4      6 [M+H]+  AA 120.0655      4 70481520 Threonine
+      4: AAs  4     26 [M+H]+  KO 120.0655      4 80851056 Threonine
+      5: AAs  4     26 [M+H]+  KO 120.0655      4 80851056 Threonine
+      6: AAs  4     26 [M+H]+  KO 120.0655      4 80851056 Threonine
+      7: AAs  4     46 [M+H]+  WT 120.0655      5 68987250 Threonine
+      8: AAs  4     46 [M+H]+  WT 120.0655      5 68987250 Threonine
+      9: AAs  4     46 [M+H]+  WT 120.0655      5 68987250 Threonine
                            SMILES qa_ms1_exists       scan ms2_sel
       1: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000058   FALSE
       2: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000059    TRUE

tests/testthat/test-plotting.R

@@ -11,8 +11,10 @@ test_that("make_eic_ms1_plot",{
     m = PLOTTING_TEST_STATE
     kvals = list(set="AAs",ID="4")
     labs = c("adduct","tag")
-    plt = make_eic_ms1_plot(db=m$db,m$db$extr$cgm$ms1,m$out$tab$summ,kvals,labs)
-    expect_equal(1,1)
+    cd = define_colrdata(m$out$tab$comp,labs)
+    plt = make_eic_ms1_plot(db=m$db,m$db$extr$cgm$ms1,m$out$tab$summ,kvals,labs,colrdata=cd)
+    plt$data = NULL
+    expect_snapshot(plt)
 })