diff --git a/NAMESPACE b/NAMESPACE
index c77cc4188e7108eb63fec131c181016a1122914a..2678e118fb789afb33a456d724cdfa8009767e1b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -31,6 +31,7 @@ export(plot_struct_nowrap)
export(prescreen)
export(read_rt)
export(report)
+export(report_old)
export(rev2list)
export(rt_input)
export(run)
diff --git a/R/api.R b/R/api.R
index f049139c3df1afbfed171c69aa3baadd5d55c2c1..9c62f734c0df5f7f5dca4fbb23df147a08ad50ea 100644
--- a/R/api.R
+++ b/R/api.R
@@ -606,7 +606,7 @@ create_plots <- function(m) {
}
#' @export
-report <- function(m) {
+report_old <- function(m) {
figtopdir <- FIG_TOPDIR #file.path(m$conf$project,FIG_TOPDIR)
pander::evalsOptions("graph.output","pdf")
author <- if (!is.null(m$conf$report$author)) m$conf$report$author else REPORT_AUTHOR
@@ -685,3 +685,87 @@ app <- function(shiny_args=list(launch.browser=F),render_args=NULL,indir=getwd()
file.copy(system.file(file.path("rmd","app.Rmd"),package = "shinyscreen"),"app_run.Rmd")
rmarkdown::run(file = "app_run.Rmd", shiny_args = shiny_args, render_args = render_args)
}
+
+
+#' @export
+#' @title report
+report <- function(m) {
+ report_author <- if (!is.null(m$conf$report$author)) m$conf$report$author else REPORT_AUTHOR
+ report_title <- if (!is.null(m$conf$report$title)) m$conf$report$title else REPORT_TITLE
+ fn_header <- system.file(file.path('rmd','report_header.rmd'),package = "shinyscreen")
+ fn_chunk <- system.file(file.path('rmd','report_chunk.rmd'), package = "shinyscreen")
+ dir.create(REP_TOPDIR,recursive = T,showWarnings = F)
+ header <- knitr::knit_expand(fn_header)
+ flt_summ <- m$out$tab$flt_summ
+ ms2 <- m$extr$ms2
+ ms1 <- m$extr$ms1
+ rt_min <- rt_in_min(m$conf$figures$rt_min)
+ rt_max <- rt_in_min(m$conf$figures$rt_max)
+ keytab <- flt_summ[,unique(.SD),.SDcol=c("adduct","ID")]
+
+ repdoc <- header
+ for (n in 1:NROW(keytab)) {
+ select <- dtable(adduct=keytab$adduct[[n]],
+ ID=keytab$ID[[n]])
+
+ pdata_ms1 <- data4plot_ms1_cgram(ms1,select)
+ pdata_ms2 <- data4plot_ms2_cgram(ms2,select)
+ pdata_spec <- data4plot_ms2_spec(ms2,flt_summ,select)
+
+ tabl_ms1 <- table_eic(pdata_ms1)
+ ## tabl_ms2 <- table_eic(pdata_ms2) # For the moment, no real
+ # info to be had here.
+ tabl_spec <- table_spec(pdata_spec)
+
+ palette = plot_palette(pdata_ms1)
+
+
+ p_eic <- plot_eic_w_facet(pdata_ms1 = pdata_ms1,
+ pdata_ms2 = pdata_ms2,
+ rt_range = c(rt_min,rt_max),
+ palette = palette) + ggplot2::theme(legend.position = "bottom")
+ p_spec <- plot_spec_w_facet(pdata_ms2 = pdata_spec,
+ mz_range = c(NA_real_,NA_real_),
+ palette = palette) + ggplot2::theme(legend.position = "bottom")
+ eic_things <- plot_save_single(p_eic,
+ decotab = select,
+ figtag = "eic",
+ proj = m$conf$project,
+ tabl = tabl_ms1,
+ subdir = REP_TOPDIR,
+ extension = m$conf$figures$ext)
+
+
+ spec_things <- plot_save_single(p_spec,
+ decotab = select,
+ figtag = "spec",
+ proj = m$conf$project,
+ tabl = tabl_spec,
+ subdir = REP_TOPDIR,
+ extension = m$conf$figures$ext)
+
+ report_chunk_header <- paste0("Adduct: ",keytab$adduct[[n]],"; ",
+ "ID: ",keytab$ID[[n]])
+
+
+ report_tab_eic_cap <- sprintf("EIC for %s",keytab$ID[[n]])
+ report_fn_eic <- eic_things$fn_plot
+ report_tab_eic <- if (shiny::isTruthy(eic_things$tab)) knitr::kable(eic_things$tab, caption = report_tab_eic_cap) else ""
+
+ report_tab_spec_cap <- sprintf("Spectrum for %s",keytab$ID[[n]])
+ report_fn_spec <- spec_things$fn_plot
+ report_tab_spec <- if (shiny::isTruthy(eic_things$tab)) knitr::kable(spec_things$tab, caption = report_tab_spec_cap) else ""
+
+ repdoc <- c(repdoc,knitr::knit_expand(fn_chunk))
+ message("(report) Knitting of chunk ",n," out of ",NROW(keytab)," has been completed.")
+
+ }
+ fn_rep <- file.path(m$conf$project,"report.Rmd")
+ message("(report) Writing Rmd...")
+ cat(repdoc,file=fn_rep,sep = "\n")
+ message("(report) ...done.")
+ message("(report) Render start ...")
+ rmarkdown::render(fn_rep,output_dir = m$conf$project)
+ message("(report) ...done.")
+ m
+}
diff --git a/R/plotting.R b/R/plotting.R
index 2ad3c3ab1e7a27e334f5bc3e2430e1d3e73e8011..0696f8a2b5550bc9cbe5871a7d198c33f6b8fc73 100644
--- a/R/plotting.R
+++ b/R/plotting.R
@@ -296,7 +296,7 @@ table_spec <- function(pdata) {
tbl
}
-plot_fname_prefix <- function(decotab,proj) {
+plot_fname_prefix <- function(decotab,proj,subdir=FIG_TOPDIR) {
if (NROW(decotab)==0) return()
adducts <- decotab[,adduct]
ids <- decotab[,ID]
@@ -308,7 +308,7 @@ plot_fname_prefix <- function(decotab,proj) {
fname <- paste(fname,chunk,sep = "_")
}
- ddir <- file.path(proj,FIG_TOPDIR)
+ ddir <- file.path(proj,subdir)
if (!dir.exists(ddir)) dir.create(ddir,recursive = T)
fname <- paste0(fname,"__id_")
@@ -319,20 +319,20 @@ plot_fname_prefix <- function(decotab,proj) {
}
-plot_save_single <- function(plot,decotab,extension,proj,tabl=NULL,figtag="") {
+plot_save_single <- function(plot,decotab,extension,proj,subdir=FIG_TOPDIR,tabl=NULL,figtag="") {
if (is.null(plot)) return()
-
- fname <- plot_fname_prefix(decotab,proj)
+
+ fname <- plot_fname_prefix(decotab,proj,subdir=subdir)
fnplot <- paste0(fname,"__",figtag,".",extension)
-
+
if (extension == "rds" || extension == "RDS") {
saveRDS(plot,file=fnplot)
} else ggplot2::ggsave(filename = fnplot,
plot = plot)
-
fntab <- paste0(fname,"__",figtag,".csv")
if (! is.null(tabl)) data.table::fwrite(tabl,file=fntab,sep = ",")
-
-
+ list(plot=plot,tab=tabl,fn_plot=fnplot)
+
}
+
diff --git a/R/resources.R b/R/resources.R
index ec273b882943bd79d09fabfeb81364983b5397c8..c11825cbbfb8b15513c8e2efcbcfe8b5a254dfa4 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -184,6 +184,7 @@ DEF_INDEX_SUMM <- c("set", "-qa_pass", "-ms1_int", "adduct","-mz")
## Top-level directory to store the figures
FIG_TOPDIR <- "figures"
+REP_TOPDIR <- "report"
## Figure filter
FIG_DEF_FILTER <- ""
diff --git a/inst/rmd/report_chunk.rmd b/inst/rmd/report_chunk.rmd
new file mode 100644
index 0000000000000000000000000000000000000000..201f66394f95a24397819cef3c32c729262371e1
--- /dev/null
+++ b/inst/rmd/report_chunk.rmd
@@ -0,0 +1,36 @@
+## {{report_chunk_header}}
+
+### EICs
+
+```{r, echo=F}
+
+if (nchar("{{report_fn_eic}}")!=0) {
+ knitr::include_graphics("{{report_fn_eic}}")
+} else {
+ "No good EIC found."
+}
+
+
+```
+
+{{report_tab_eic}}
+
+
+
+### MS2 Spectrum
+
+```{r, echo=F}
+
+if (nchar("{{report_fn_spec}}")!=0) {
+ knitr::include_graphics("{{report_fn_spec}}")
+} else {
+ "No good MS2 spectrum found."
+}
+
+```
+
+
+{{report_tab_spec}}
+
+
+\newpage
diff --git a/inst/rmd/report_header.rmd b/inst/rmd/report_header.rmd
new file mode 100644
index 0000000000000000000000000000000000000000..8cf1521ca8f8e1cfea9e6292732db88fb3edff21
--- /dev/null
+++ b/inst/rmd/report_header.rmd
@@ -0,0 +1,13 @@
+---
+output:
+ pdf_document:
+ extra_dependencies: ["float"]
+
+author: "{{report_author}}"
+title: "{{report_title}}"
+geometry: margin=0.5cm
+---
+
+```{r, echo=F}
+knitr::opts_chunk$set(fig.pos = "!H", out.extra = "")
+```
diff --git a/man/report.Rd b/man/report.Rd
new file mode 100644
index 0000000000000000000000000000000000000000..6e1d8a76a5e1edd67b0fedbd06546cecf9c816a4
--- /dev/null
+++ b/man/report.Rd
@@ -0,0 +1,11 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/api.R
+\name{report}
+\alias{report}
+\title{report}
+\usage{
+report(m)
+}
+\description{
+report
+}