Test for `narrow_summ' and start testing `make_eic_ms1_plot'.

tests/testthat/_snaps/plotting.md

+# narrow_summ
+
+    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
+                           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
+      3: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000060   FALSE
+      4: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000267   FALSE
+      5: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000268    TRUE
+      6: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000269   FALSE
+      7: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000477   FALSE
+      8: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000478    TRUE
+      9: C[C@@H](O)[C@H](N)C(O)=O          TRUE F1.S000479   FALSE
+

tests/testthat/setup-plotting.R

 
 
 
-PLOTTING_STATE = readRDS(system.file(package="shinyscreen","testdata","plotting-state.rds"))
+pre_test_state = readRDS(system.file(package="shinyscreen","testdata","plotting-state.rds"))
 
 
 synthetise_cgm_ms1 <- function(n,fac,shift) {
@@ -127,3 +127,8 @@ fix_testing_state_conf <- function(conf) {
 ##     dt = empty_cgram_ms1(
 ## }
 
+pre_test_state$db = synthetise_pseudo_state_db(pre_test_state$db)
+pre_test_state$conf = fix_testing_state_conf(pre_test_state$conf)
+pre_test_state = prescreen(pre_test_state)
+PLOTTING_TEST_STATE = pre_test_state
+rm(pre_test_state)

tests/testthat/test-plotting.R

-test_that("get_data_from_key",{
-    m = PLOTTING_STATE
-    m$db = synthetise_pseudo_state_db(m$db)
-    m$conf = fix_testing_state_conf(m$conf)
-    m = prescreen(m)
-    browser()
-    expect_identical(1L,1L)
+test_that("narrow_summ",{
+    m = PLOTTING_TEST_STATE
+    ## kvals =  list(set="AAs",ID="5") # 5 is interesting (isobars with 19)
+    kvals = list(set="AAs",ID="4")
+    labs = c("adduct","tag")
+    ns = narrow_summ(db=m$db,m$out$tab$summ,kvals,labs,"mz","ms1_rt","ms1_int","Name","SMILES","qa_ms1_exists","scan","ms2_sel")
+    expect_snapshot(ns)
+})
+
+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)
 })