From 53cfda9fb5f6b2bb8f1ac667c6b15a7f18123996 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Mon, 27 Feb 2023 13:46:01 +0100
Subject: [PATCH] Try to set proper default values for tag_sets_list and
tag_adducts_list.
---
R/resources.R | 188 +++++++++++++++++++--------------------
R/shiny-ui-base.R | 60 +++++++++----
inst/rmd/app_project.Rmd | 14 +--
3 files changed, 146 insertions(+), 116 deletions(-)
diff --git a/R/resources.R b/R/resources.R
index 6023e46..c534c47 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -16,35 +16,35 @@
## Config defaults
-CONF <- list(data=NA_character_,
+CONF = list(data=NA_character_,
project=getwd(),
compounds=list(lists=list(),
sets=NA_character_))
## Constants
FN_ENVOPTS="envopts.rds"
-FN_SUMM_BASE<-"summ.base.csv"
-FN_SUMM_PP<-"summ.pp.csv"
-FN_PP_OUT_PREF<-"PP.filetable"
-FN_SUMM_STATE<-"summ_state.csv"
-FN_SUMM <- "summ.csv"
-FN_SUMM_DEF_OUT <- FN_SUMM
-FN_CMP_L<-"compounds.csv"
-FN_LOC_SETID <-"setid.csv"
-FN_COMP_TAB<-"comprehensive.csv"
-FN_SPEC<-"specdata.rds"
-FN_CONF <- "conf-state.yaml"
-FN_EXTR_STATE <- "state_after_extraction.rds"
-FN_STATE <- "current-state.rds"
-FN_GUI_STATE <- "gui.rds"
-.envp <- new.env(parent = emptyenv())
+FN_SUMM_BASE="summ.base.csv"
+FN_SUMM_PP="summ.pp.csv"
+FN_PP_OUT_PREF="PP.filetable"
+FN_SUMM_STATE="summ_state.csv"
+FN_SUMM = "summ.csv"
+FN_SUMM_DEF_OUT = FN_SUMM
+FN_CMP_L="compounds.csv"
+FN_LOC_SETID ="setid.csv"
+FN_COMP_TAB="comprehensive.csv"
+FN_SPEC="specdata.rds"
+FN_CONF = "conf-state.yaml"
+FN_EXTR_STATE = "state_after_extraction.rds"
+FN_STATE = "current-state.rds"
+FN_GUI_STATE = "gui.rds"
+.envp = new.env(parent = emptyenv())
data(adducts,package = "enviPat", envir = .envp)
data(isotopes,package = "enviPat", envir = .envp)
-ADDUCTS <- dtable(.envp$adducts)
-ISOTOPES <- dtable(.envp$isotopes)
-.envp <- NULL
-ADDUCTMAP <- ADDUCTS$Name
-ADDUCTS$Name <- the_ifelse(ADDUCTS$Charge>0,paste0("[",ADDUCTS$Name,"]+"),paste0("[",ADDUCTS$Name,"]-"))
+ADDUCTS = dtable(.envp$adducts)
+ISOTOPES = dtable(.envp$isotopes)
+.envp = NULL
+ADDUCTMAP = ADDUCTS$Name
+ADDUCTS$Name = the_ifelse(ADDUCTS$Charge>0,paste0("[",ADDUCTS$Name,"]+"),paste0("[",ADDUCTS$Name,"]-"))
## names(ADDUCTMAP) <- apply(ADDUCTS,1,function(row) {
## nm <- row[["Name"]]
## sgn <- row[["Charge"]]
@@ -52,68 +52,68 @@ ADDUCTS$Name <- the_ifelse(ADDUCTS$Charge>0,paste0("[",ADDUCTS$Name,"]+"),paste0
## paste0("[",nm,"]",suff)
## })
## ADDUCTS$Name <- names(ADDUCTMAP)
-DISP_ADDUCTS <- ADDUCTS$Name
-TAG_NA <- "::UNSET::"
-SET_NA <- "::UNSET::"
-TAG_DEF <- TAG_NA
-TAG_DEF_DESC<-"Case"
+DISP_ADDUCTS = ADDUCTS$Name
+TAG_NA = "::UNSET::"
+SET_NA = "::UNSET::"
+TAG_DEF = TAG_NA
+TAG_DEF_DESC="Case"
DEFAULT_RT_RANGE=c(NA,NA)
DEFAULT_INT_RANGE=c(NA,NA)
DEFAULT_MZ_RANGE=c(NA,NA)
-## QANAMES <- c("MS1","MS2","Alignment","AboveNoise")
-PLOT_DEF_TAGS<-NA
-PLOT_DEF_SET<-NA
+## QANAMES = c("MS1","MS2","Alignment","AboveNoise")
+PLOT_DEF_TAGS=NA
+PLOT_DEF_SET=NA
-CEX<-0.75
+CEX=0.75
RT_DIGITS=2
M_DIGITS=4
PAL="Dark2"
-REST_TAB<-c("mzml")
+REST_TAB=c("mzml")
-GUI_TAB_TITLE<-c(conf="Config",
+GUI_TAB_TITLE=c(conf="Config",
gen="Spectra Extraction and Automatic QA",
pres="Prescreening",
log="Log")
-GUI_SIDE_TITLE<-GUI_TAB_TITLE
-GUI_SIDE_TITLE[["gen"]]<-"Spectra Extraction"
+GUI_SIDE_TITLE=GUI_TAB_TITLE
+GUI_SIDE_TITLE[["gen"]]="Spectra Extraction"
CHR_GRAM_X="retention time [min]"
CHR_GRAM_Y="intensity"
KEY_GLYPH='rect'
-PLOT_MS1_LEG_TIT<-"peak retention time (MS1)"
-PLOT_MS2_LEG_TIT<-"peak retention time (MS2)"
+PLOT_MS1_LEG_TIT="peak retention time (MS1)"
+PLOT_MS2_LEG_TIT="peak retention time (MS2)"
-MS2_1ST_N<-5
+MS2_1ST_N=5
-EXTR_MS2_DIR<-"MS2"
-EXTR_MS2_FLAG<-file.path(EXTR_MS2_DIR,'.ms2.DONE')
+EXTR_MS2_DIR="MS2"
+EXTR_MS2_FLAG=file.path(EXTR_MS2_DIR,'.ms2.DONE')
-SUMM_CHK_NONE<-'NONE'
+SUMM_CHK_NONE='NONE'
-SUMM_CHK_AUTO<-'AUTO'
+SUMM_CHK_AUTO='AUTO'
-SUMM_CHK_MANL<-'MANUAL'
+SUMM_CHK_MANL='MANUAL'
-MS1_ERR_COARSE<-"0.5 Da" # Da
-MS1_ERR_FINE<- "5 ppm" # ppm
-EIC_ERR <- "0.001 Da" # Da
-RT_EXTR_ERR<-"0.5 min" # min
-RT_SHIFT_ERR <- "0.5 min" # min
+MS1_ERR_COARSE="0.5 Da" # Da
+MS1_ERR_FINE= "5 ppm" # ppm
+EIC_ERR = "0.001 Da" # Da
+RT_EXTR_ERR="0.5 min" # min
+RT_SHIFT_ERR = "0.5 min" # min
-MS1_INT_THOLD <- 1e5
-MS2_INT_THOLD <- 2500.
+MS1_INT_THOLD = 1e5
+MS2_INT_THOLD = 2500.
-MS1_SN_FAC <- 3.0
+MS1_SN_FAC = 3.0
## Shiny objects
@@ -124,7 +124,7 @@ NUM_INP_HEIGHT="5%"
## Possible compound list fields
-EMPTY_CMPD_LIST <- dtable(ID=character(),
+EMPTY_CMPD_LIST = dtable(ID=character(),
SMILES=character(),
Name=character(),
Formula=character(),
@@ -132,32 +132,32 @@ EMPTY_CMPD_LIST <- dtable(ID=character(),
mz=numeric(),
known=character(),
ORIG=character())
-COMP_LIST_COLS <- c("ID","Name","SMILES","Formula","RT","mz")
+COMP_LIST_COLS = c("ID","Name","SMILES","Formula","RT","mz")
## Comprehensive table properties
-COMP_NAME_MAP <- list(RT="rt")
-COMP_NAME_FIRST <- c("ID","mz","rt","adduct","tag","set","Name","known","SMILES","Formula","file")
+COMP_NAME_MAP = list(RT="rt")
+COMP_NAME_FIRST = c("ID","mz","rt","adduct","tag","set","Name","known","SMILES","Formula","file")
## Trivial data table
-EMPTY_MZML <- dtable(file=character(0),
+EMPTY_MZML = dtable(file=character(0),
tag=character(0),
adduct=character(0),
set=character(0))
-FN_DATA_TAB <- "data-files.csv"
+FN_DATA_TAB = "data-files.csv"
## Default number of concurrent workers
-NO_WORKERS <- 2
+NO_WORKERS = 2
## Input parameters for prescreening.
-CONF_PRES_NUM <- c("ms1_int_thresh","ms2_int_thresh","s2n")
-CONF_PRES_TU <- c("ret_time_shift_tol")
+CONF_PRES_NUM = c("ms1_int_thresh","ms2_int_thresh","s2n")
+CONF_PRES_TU = c("ret_time_shift_tol")
## Prescreening columns
-QA_FLAGS <- c("qa_pass",
+QA_FLAGS = c("qa_pass",
"qa_ms1_exists",
"qa_ms2_exists",
"qa_ms1_good_int",
@@ -165,7 +165,7 @@ QA_FLAGS <- c("qa_pass",
"qa_ms2_near",
"qa_ms2_good_int")
-QABOX_VALS <- c("MS1 exists"="qa_ms1_exists",
+QABOX_VALS = c("MS1 exists"="qa_ms1_exists",
"MS1 good intensity"="qa_ms1_good_int",
"MS1 above noise"="qa_ms1_above_noise",
"MS2 exists"="qa_ms2_exists",
@@ -173,42 +173,42 @@ QABOX_VALS <- c("MS1 exists"="qa_ms1_exists",
"MS2 no RT shift"="qa_ms2_near")
-QA_NUM_REAL <- c("ms1_int","ms1_rt","ms1_mean")
+QA_NUM_REAL = c("ms1_int","ms1_rt","ms1_mean")
-QA_NUM_INT <- c("ms2_sel","ms1_rt_ind")
+QA_NUM_INT = c("ms2_sel","ms1_rt_ind")
-QA_COLS <- c(QA_FLAGS,QA_NUM_REAL,QA_NUM_INT)
+QA_COLS = c(QA_FLAGS,QA_NUM_REAL,QA_NUM_INT)
## MS2 spectral table columns
-MS2_SPEC_COLS <- c("adduct","tag","ID","CE","rt","file","spec","ms2_max_int")
+MS2_SPEC_COLS = c("adduct","tag","ID","CE","rt","file","spec","ms2_max_int")
## MS1 spectral table columns
-MS1_SPEC_COLS <- c("adduct","tag","ID","eicMS1","ms1_int","ms1_rt","ms1_mean")
+MS1_SPEC_COLS = c("adduct","tag","ID","eicMS1","ms1_int","ms1_rt","ms1_mean")
## Default secondary indexing in the summary table
-DEF_INDEX_SUMM <- c("set", "-qa_pass", "-ms1_int", "adduct","-mz")
+DEF_INDEX_SUMM = c("set", "-qa_pass", "-ms1_int", "adduct","-mz")
## Top-level directory to store the figures
-FIG_TOPDIR <- "figures"
+FIG_TOPDIR = "figures"
-REP_TOPDIR <- "report"
+REP_TOPDIR = "report"
## Figure filter
-FIG_DEF_FILTER <- ""
+FIG_DEF_FILTER = ""
-FIG_DEF_SUBSET <- c("set","adduct","ID")
+FIG_DEF_SUBSET = c("set","adduct","ID")
-REPORT_AUTHOR <- "Anonymous"
-REPORT_TITLE <- "Plots of EICs and MS2 Spectra"
+REPORT_AUTHOR = "Anonymous"
+REPORT_TITLE = "Plots of EICs and MS2 Spectra"
## Select the most fundamental group of entries. Within this group,
## each ID is unique.
-BASE_KEY <- c("adduct","tag","ID")
-BASE_KEY_MS2 <- c(BASE_KEY,"CE","an")
+BASE_KEY = c("adduct","tag","ID")
+BASE_KEY_MS2 = c(BASE_KEY,"CE","an")
-FIG_DEF_CONF <-list(grouping=list(group="adduct",
+FIG_DEF_CONF =list(grouping=list(group="adduct",
plot="ID",
label="tag"))
@@ -217,14 +217,14 @@ FIG_DEF_CONF <-list(grouping=list(group="adduct",
SUMM_COLS=c("set",BASE_KEY_MS2,"mz","ms1_rt", "ms1_int", "ms2_rt", "ms2_int",
"ms1_mean","ms2_sel",QA_FLAGS,"Name", "SMILES", "Formula", "known","Comments","file")
-SUMM_KEY <- c("set","ID","adduct","tag","an")
+SUMM_KEY = c("set","ID","adduct","tag","an")
-PLOT_FEATURES <- c("adduct",
+PLOT_FEATURES = c("adduct",
"tag",
"ID")
## Empty summary table.
-EMPTY_SUMM <- data.table::data.table(set=character(0),
+EMPTY_SUMM = data.table::data.table(set=character(0),
adduct=character(0),
tag=character(0),
ID=character(0),
@@ -252,10 +252,10 @@ EMPTY_SUMM <- data.table::data.table(set=character(0),
file=character(0))
## Default sorting keys of spectra in the summary table
-DEF_KEY_SUMM <- c(BASE_KEY_MS2,"an")
+DEF_KEY_SUMM = c(BASE_KEY_MS2,"an")
-SUBSET_VALS <- c(IGNORE="ignore",
+SUBSET_VALS = c(IGNORE="ignore",
GOOD="select good",
BAD="select bad")
@@ -263,7 +263,7 @@ SUBSET_VALS <- c(IGNORE="ignore",
## Empty comprehensive table.
-EMPTY_COMP_TAB <- dtable(ID=character(),
+EMPTY_COMP_TAB = dtable(ID=character(),
mz=numeric(),
rt=numeric(),
adduct=character(),
@@ -276,13 +276,13 @@ EMPTY_COMP_TAB <- dtable(ID=character(),
file=character())
-DEF_CONF_MISSING_PCS <- "do_nothing"
+DEF_CONF_MISSING_PCS = "do_nothing"
## Significant digits for output
-SIGNF_I <- 3
-SIGNF_MZ <- 7
-SIGNF_RT <- 4
+SIGNF_I = 3
+SIGNF_MZ = 7
+SIGNF_RT = 4
## Symbols to display T, or F
@@ -290,13 +290,13 @@ SYM_YES="\U002713"
SYM_NO="\U00274C"
-CMPD_LIST_PATT <- "((*.csv)|(*.csv.gz))$"
-SET_LIST_PATT <- CMPD_LIST_PATT
-DFILES_LIST_PATT <- ".*\\.mz[Mm][Ll]$"
+CMPD_LIST_PATT = "((*.csv)|(*.csv.gz))$"
+SET_LIST_PATT = CMPD_LIST_PATT
+DFILES_LIST_PATT = ".*\\.mz[Mm][Ll]$"
-CINDEX_BY <- c("set","ID","adduct","tag")
-CINDEX_COLS <- c("mz", "ms1_rt","Name","qlt_ms1","qlt_ms2")
-ARRANGE_CHOICES <- c(nothing="nothing",
+CINDEX_BY = c("set","ID","adduct","tag")
+CINDEX_COLS = c("mz", "ms1_rt","Name","qlt_ms1","qlt_ms2")
+ARRANGE_CHOICES = c(nothing="nothing",
quality="quality",
set="set",
adduct="adduct",
@@ -304,12 +304,12 @@ ARRANGE_CHOICES <- c(nothing="nothing",
rt="rt",
id="ID")
-PLOT_EIC_ASPECT <- 0.75
+PLOT_EIC_ASPECT = 0.75
## Each set should have it's different colourscheme, because of the
## possibility that each set connects to a different collection of
## files.
-COLRDATA_KEY <- "set"
+COLRDATA_KEY = "set"
## METFRAG
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index eb07a3a..05946ad 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -1057,14 +1057,15 @@ mk_shinyscreen_server <- function(projects,init) {
rvs$gui$compounds$sets = sels
})
- observeEvent(rvs$gui$datatab$set,{
- if (isTruthy(rvs$gui$datatab$set)) {
+ observeEvent(rf_get_sets(),{
+ sets = rf_get_sets()
+ if (isTruthy(rf_get_sets())) {
updateSelectInput(session=session,
- inputId="tag_set_list",
- choices=rvs$gui$datatab$set,
- selected=NA_character_)
+ inputId="tag_sets_list",
+ choices=sets,
+ selected=NULL)
}
- }, label="tag_set_list")
+ }, label="tag_sets_list")
observeEvent(input$datafiles_b,{
new_file = input$dfile_list
@@ -1113,15 +1114,41 @@ mk_shinyscreen_server <- function(projects,init) {
}, label = "datafiles-edit")
- observeEvent(input$datatab_cell_edit,{
- df = gen_dtab(rvs$gui$datatab,sets=rf_get_sets())
- z = DT::editData(df,
- input$datatab_cell_edit,
- rownames = F)
+ ## observeEvent(input$datatab_cell_edit,{
+ ## df = gen_dtab(rvs$gui$datatab,sets=rf_get_sets())
+ ## z = DT::editData(df,
+ ## input$datatab_cell_edit,
+ ## rownames = F)
- rvs$gui$datatab$set = z$set
- rvs$gui$datatab$adduct = z$adduct
- }, label = "datatab-edit")
+ ## rvs$gui$datatab$set = z$set
+ ## rvs$gui$datatab$adduct = z$adduct
+ ## }, label = "datatab-edit")
+
+ observe({
+ selected_adducts = input$tag_adducts_list
+ ## selected_adducts[selected_adducts == "NA"] = NA_character_
+ selected_sets = input$tag_sets_list
+ ## selected_sets[selected_sets == "NA"] = NA_character_
+ selected_rows = input$datafiles_rows_selected
+ if (isTruthy(selected_rows)) {
+ selected_tags = rvs$gui$datafiles$tag[selected_rows]
+ dt_rows = which(rvs$gui$datatab$tag %in% selected_tags)
+ if (isTruthy(selected_sets)) {
+ rvs$gui$datatab$set[dt_rows] = selected_sets
+ updateSelectInput(session=session,
+ inputId="tag_adducts_list",
+ selected=NULL)
+ }
+
+ if (isTruthy(selected_adducts)) {
+ rvs$gui$datatab$adduct[dt_rows] = selected_adducts
+ updateSelectInput(session=session,
+ inputId="tag_sets_list",
+ selected=NULL)
+ }
+ }
+
+ }, label = "datatab-set-associations")
## OBSERVERS: CONFIGURATION AND EXTRACTION
@@ -1583,8 +1610,9 @@ mk_shinyscreen_server <- function(projects,init) {
sets = rf_get_sets()
dtab = gen_dtab(rvs$gui$datatab,
sets=sets)
- tab = scroll_dropdown_dt(dtab, callback = dt_drop_callback('1','2',sets))
- ## tab = dropdown_dt(dtab, callback = dt_drop_callback('1','2',sets))
+ ## tab = scroll_dropdown_dt(dtab, callback = dt_drop_callback('1','2',sets))
+ tab = scroll_style_dt(dtab)
+
tab
})
diff --git a/inst/rmd/app_project.Rmd b/inst/rmd/app_project.Rmd
index 77c7599..241bf44 100644
--- a/inst/rmd/app_project.Rmd
+++ b/inst/rmd/app_project.Rmd
@@ -264,16 +264,18 @@ Repeat the same for sets.
</details>
```{r, echo=F}
+selectInput(inputId="tag_sets_list",
+ label="Select set",
+ ## multiple=T, #TODO
+ choices=NULL,
+ selected=NULL)
+```
+```{r, echo=F}
selectInput(inputId="tag_adducts_list",
label="Select adducts",
choices=shinyscreen:::DISP_ADDUCTS,
multiple=T,
- selected=NA_character_)
-```
-```{r, echo=F}
-selectInput(inputId="tag_set_list",
- label="Select set",
- choices=NULL)
+ selected=NULL)
```
<!-- tag/adduct/set associations -->
</div>
--
GitLab