From 32e64b9847e2a6d9f4b2d0e8150733966692b34e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <kontrapunkt@uclmail.net>
Date: Sun, 18 Dec 2022 15:01:10 +0100
Subject: [PATCH] api, mix, plotting: Fix unknown SMILES/Formulas plots.
---
DESCRIPTION | 2 +-
NAMESPACE | 1 -
R/api.R | 29 ++++-------------------------
R/mix.R | 6 +++++-
R/plotting.R | 31 ++++++++++++++++++++++++-------
R/shiny-ui-base.R | 11 ++---------
6 files changed, 36 insertions(+), 44 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index b94ce0a..1953c5f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: shinyscreen
Title: Pre-screening of Mass Spectrometry Data
-Version: 1.2.1
+Version: 1.2.2
Author: Todor Kondić
Maintainer: Todor Kondić <todor.kondic@uni.lu>
Authors@R:
diff --git a/NAMESPACE b/NAMESPACE
index fe8b0e5..ec49d63 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,7 +7,6 @@ export(create_plots)
export(create_stub_gui)
export(extr_data)
export(extract)
-export(gen_struct_plots)
export(get_fn_comp)
export(get_fn_conf)
export(get_fn_extr)
diff --git a/R/api.R b/R/api.R
index 65d7014..20a3fe3 100644
--- a/R/api.R
+++ b/R/api.R
@@ -192,6 +192,10 @@ mk_comp_tab <- function(m) {
}
smiforadd <- smiles[smiforadd,.(ID,SMILES,Formula,adduct),on=c("SMILES")]
data.table::setkey(smiforadd,"adduct","ID")
+
+ ## FIXME: Why is Formula a list when there are no SMILES, instead
+ ## of an empty string?
+ smiforadd[,Formula:=as.character(Formula)]
## Update the intermediate table with masses.
message("Formulas have been calculated. Start calculating masses from formulas.")
@@ -611,31 +615,6 @@ subset_summary <- function(m) {
m
}
-
-##' @export
-gen_struct_plots <- function(m) {
- ## Generate structure plots.
- comp <- m$out$tab$comp
-
- res <- if (NROW(comp)>0) {
- structtab <- m$out$tab$comp[known=="structure",unique(.SD),.SDcols=c("ID","SMILES")]
- message("Start generating structures.")
- if (NROW(structtab)>0) {
- structtab[,img:=.({tmp <- lapply(SMILES,function (sm) smiles2img(sm,width = 500,height = 500, zoom = 4.5))
- tmp})]
- message("Done generating structures.")
- structtab
- } else dtable(ID=character(0),SMILES=character(0),img=list())
- } else {
- dtable(ID=character(0),SMILES=character(0),img=list())
- }
-
- m$out$tab$structfig <- res
-
- m
-}
-
-
#' @export
create_plots <- function(m) {
## Produce plots of EICs and spectra and group them acording to
diff --git a/R/mix.R b/R/mix.R
index 69176c7..aa88970 100644
--- a/R/mix.R
+++ b/R/mix.R
@@ -132,6 +132,9 @@ calc_mz_from_formula <- function(chform,adduct,id) {
smiles2form <- function(smiles) {
+ res <- character(length(smiles))
+ res <- NA_character_
+ isomething <- which(!is.na(smiles) | nchar(smiles) > 0L)
one2form <- function (s) {
mol <- try(RMassBank::getMolecule(s), silent = T)
if (!is.atomic(mol)) {
@@ -139,7 +142,8 @@ smiles2form <- function(smiles) {
} else ""
}
- sapply(smiles,one2form,USE.NAMES = F)
+ res[isomething] <- sapply(smiles[isomething],one2form,USE.NAMES = F)
+ res
}
diff --git a/R/plotting.R b/R/plotting.R
index 0f1004d..e98256f 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -101,18 +101,35 @@ pal_maker <- function(n,palname = NULL) {
}
### PLOTTING: AESTHETIC FUNCTIONS
-smiles2img <- function(smiles, kekulise=TRUE, width=300, height=300,
+
+
+make_struct_plot <- function(smiles, kekulise=TRUE, width=300, height=300,
zoom=1.3,style="cow", annotate="off", abbr="on",suppressh=TRUE,
showTitle=FALSE, smaLimit=100, sma=NULL) {
- dep <- rcdk::get.depictor(width = width, height = height, zoom = zoom, style = style, annotate = annotate,
- abbr = abbr, suppressh = suppressh, showTitle = showTitle, smaLimit = smaLimit,
- sma = NULL)
- mol <- RMassBank::getMolecule(smiles)
- z<-rcdk::view.image.2d(mol, depictor=dep)
- grid::rasterGrob(z)
+ ## structure -> grob
+ smiles2img <- function() {
+ if (is.na(smiles) || nchar(smiles)==0) return(NULL) #Handle empty SMILES.
+ dep <- rcdk::get.depictor(width = width, height = height, zoom = zoom, style = style, annotate = annotate,
+ abbr = abbr, suppressh = suppressh, showTitle = showTitle, smaLimit = smaLimit,
+ sma = NULL)
+
+ mol <- RMassBank::getMolecule(smiles)
+ z<-rcdk::view.image.2d(mol, depictor=dep)
+ grid::rasterGrob(z)
+ }
+
+ grob <- smiles2img()
+
+ if (!is.null(grob)) {
+ qplot(1:5, 2*(1:5), geom="blank") +
+ annotation_custom(grob, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
+ theme_empty
+ } else NULL
+
}
+
guide_fun <- function() {
## ggplot2::guides(colour=ggplot2::guide_legend(nrow=2,
## byrow=T,
diff --git a/R/shiny-ui-base.R b/R/shiny-ui-base.R
index c730e22..05702e1 100644
--- a/R/shiny-ui-base.R
+++ b/R/shiny-ui-base.R
@@ -871,11 +871,7 @@ mk_shinyscreen_server <- function(projects,init) {
row <- req(input$cindex_row_last_clicked)
id <- rowtab <- cind[row][,..key][["ID"]][[1]]
smi <- rvs$m$out$tab$comp[ID==(id),SMILES][[1]]
- grb <- smiles2img(smi)
- xx <- qplot(1:5, 2*(1:5), geom="blank") +
- annotation_custom(grb, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
- theme_empty
- xx
+ make_struct_plot(smi)
})
rf_plot_spec_ms2 <- reactive({
@@ -1260,10 +1256,7 @@ mk_shinyscreen_server <- function(projects,init) {
id <- rowtab <- cind[ri][,..key][["ID"]][[1]]
smi <- rvs$m$out$tab$comp[ID==(id),SMILES][[1]]
- grb <- smiles2img(smi)
- p_struc <- qplot(1:5, 2*(1:5), geom="blank") +
- annotation_custom(grb, xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
- theme_empty
+ p_struc <- make_struct_plot(smi)
p_spec <- make_spec_ms2_plot(ms2,
summ,
--
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