From faad974bc7af3648ef2f895a9dbebe29573bc4d3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Tue, 12 Jul 2022 15:58:58 +0200
Subject: [PATCH] app: Sorting compound index works.
---
R/mix.R | 19 +++++++++++--------
R/resources.R | 10 ++++++++--
R/shiny-state.R | 2 +-
R/shiny-ui-base.R | 30 ++++++++++++++++++------------
inst/rmd/app.Rmd | 2 +-
5 files changed, 39 insertions(+), 24 deletions(-)
diff --git a/R/mix.R b/R/mix.R
index 377aa11..e1afbcd 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -196,14 +196,17 @@ gen_summ <- function(comp,qa_ms1,qa_ms2) {
data.table::setcolorder(summ,SUMM_COLS)
## Quality scores for ms1 and ms2.
- summ[,qa_ms1 := Map(function(m1,m2,m3) { m1*5L + m2*3L + m3*2L},
- as.integer(qa_ms1_exists),
- as.integer(qa_ms1_above_noise),
- as.integer(qa_ms1_good_int))]
- summ[,qa_ms2 := Map(function(m1,m2,m3) { m1*5L + m2*3L + m3*2L},
- as.integer(qa_ms2_exists),
- as.integer(qa_ms2_near),
- as.integer(qa_ms2_good_int))]
+ summ[,qa_ms1 := as.integer(Map(function(m1,m2,m3) { m1*5L + m2*3L + m3*2L},
+ as.integer(qa_ms1_exists),
+ as.integer(qa_ms1_above_noise),
+ as.integer(qa_ms1_good_int)))]
+ summ[,qa_ms2 := as.integer(Map(function(m1,m2,m3) { m1*5L + m2*3L + m3*2L},
+ as.integer(qa_ms2_exists),
+ as.integer(qa_ms2_near),
+ as.integer(qa_ms2_good_int)))]
+
+ summ[is.na(qa_ms1),qa_ms1:=0L]
+ summ[is.na(qa_ms2),qa_ms2:=0L]
summ
diff --git a/R/resources.R b/R/resources.R
index 2b131ab..0b52be1 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -284,5 +284,11 @@ SET_LIST_PATT <- CMPD_LIST_PATT
DFILES_LIST_PATT <- ".*\\.mz[Mm][Ll]$"
CINDEX_BY <- c("set","adduct","tag","ID")
-CINDEX_COLS <- c("mz", "ms1_rt", "Formula","Name")
-ARRANGE_CHOICES <- c(NA_character_,"quality","set", "adduct", "tag", "mz", "rt")
+CINDEX_COLS <- c("mz", "ms1_rt", "Formula","Name","qa_ms1","qa_ms2")
+ARRANGE_CHOICES <- c(nothing="nothing",
+ quality="quality",
+ set="set",
+ adduct="adduct",
+ tag="tag",
+ mz="mz",
+ rt="ms1_rt")
diff --git a/R/shiny-state.R b/R/shiny-state.R
index d8e3ca3..3a2a252 100644
--- a/R/shiny-state.R
+++ b/R/shiny-state.R
@@ -335,7 +335,7 @@ pre_setup_val_block <- function(gui) {
T
}
-gen_cindex <- function(summ,cols = CINDEX_COLS,by. = CINDEX_BY, sort=character(0)) {
+gen_cindex <- function(summ,cols = CINDEX_COLS,by. = CINDEX_BY) {
allc <- c(by.,cols)
res <- summ[,first(.SD),by=by.][,..allc]
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index a9fef10..bc8653b 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -704,29 +704,35 @@ mk_shinyscreen_server <- function(projects,init) {
m$input$tab$setid
})
- rf_get_cindex <- eventReactive(rvs$status$is_qa_stat,{
+ rf_get_cindex <- reactive({
+ rvs$status$is_qa_stat
+ s1 <- input$sort1
+ s2 <- input$sort2
+ s3 <- input$sort3
+ s4 <- input$sort4
summ <- req(rvs$m$out$tab$summ)
+ isolate({
if (NROW(summ)>0L) {
- s1 <- input$sort1
- s2 <- input$sort2
- s3 <- input$sort3
- s4 <- input$sort4
sortorder <- unique(c(s1,s2,s3,s4))
- message("----")
- message(paste0(sortorder,collapse=','))
- wna <- which(is.na(sortorder)); if (length(wna)>0L) sortorder <- sortorder[-wna]
- message(paste0(sortorder,collapse=','))
+ wna <- which(sortorder=="nothing"); if (length(wna)>0L) sortorder <- sortorder[-wna]
quality <- which("quality"==sortorder)
if (length(quality)>0L) {
pre <- head(sortorder,quality-1L)
- post <- tail(sortorder,quality+1L)
+ post <- tail(sortorder,-quality)
sortorder <- c(pre,"qa_ms1","qa_ms2",post)
}
- message(paste0(sortorder,collapse=','))
- setorderv(gen_cindex(summ),cols=sortorder)
+
+
+ ord <- rep(1L,length(sortorder))
+ if ("qa_ms1" %in% sortorder) {
+ ind <- which(sortorder %in% c("qa_ms1","qa_ms2"))
+ ord[ind] <- -1L
+ }
+ setorderv(gen_cindex(summ),cols=sortorder,order=ord)
} else {
NULL
}
+ })
})
diff --git a/inst/rmd/app.Rmd b/inst/rmd/app.Rmd
index 007d9b9..c5330eb 100644
--- a/inst/rmd/app.Rmd
+++ b/inst/rmd/app.Rmd
@@ -642,7 +642,7 @@ DT::dataTableOutput("setid_table")
<div style="display: flex; flex-flow: row wrap;">
-<div style="width: 25%; padding-right: 1.0em; background-color: var(--lt-gr-bg);">
+<div style="width: 25%; padding-right: 1.0em; background-color: var(--lt-gr-bg); overflow-y: scroll">
<div>
### Compound Index
--
GitLab