From cce27875bc2c5ec2825c6a92e84f2aae4ae3de3d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Mon, 10 Apr 2023 18:23:40 +0200
Subject: [PATCH] Cleaned up make_eic_ms1_plot and related functions.
---
R/plotting.R | 25 +++++++++++--------------
tests/testthat/_snaps/plotting.md | 20 ++++++++++----------
tests/testthat/test-plotting.R | 6 ++++--
3 files changed, 25 insertions(+), 26 deletions(-)
diff --git a/R/plotting.R b/R/plotting.R
index 69b0c50..349dfaa 100644
--- a/R/plotting.R
+++ b/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]
diff --git a/tests/testthat/_snaps/plotting.md b/tests/testthat/_snaps/plotting.md
index 8d529dd..155d599 100644
--- a/tests/testthat/_snaps/plotting.md
+++ b/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
diff --git a/tests/testthat/test-plotting.R b/tests/testthat/test-plotting.R
index 4b16e91..cd51c65 100644
--- a/tests/testthat/test-plotting.R
+++ b/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)
})
--
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