From 9b9e93930966ed58cd305bc77a78b8155a589310 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Fri, 11 Dec 2020 10:04:59 +0100
Subject: [PATCH] api: Remove obsolete save_plots
---
R/api.R | 114 +-------------------------------------------------------
1 file changed, 1 insertion(+), 113 deletions(-)
diff --git a/R/api.R b/R/api.R
index 4878a9a..57b3416 100644
--- a/R/api.R
+++ b/R/api.R
@@ -37,8 +37,7 @@ run <- function(fn_conf="",m=NULL,phases=NULL,help=F) {
prescreen=prescreen,
sort=sort_spectra,
subset=subset_summary,
- plot=create_plots,
- saveplot=save_plots)
+ plot=create_plots)
if (help) {
message("(run): You can run some of the following, or all the phases:")
@@ -84,7 +83,6 @@ run_in_dir <- function(m) {
m <- sort_spectra(m)
m <- subset_summary(m)
m <- create_plots(m)
- m <- save_plots(m)
invisible(m)
}
@@ -633,116 +631,6 @@ create_plots <- function(m) {
m
}
-#' @export
-save_plots <- function(m) {
- topdir <- FIG_TOPDIR
- dir.create(topdir,showWarnings = F)
-
- my_theme <- function(...) plot_theme(legend.position = "left",
- legend.direction = "vertical")
-
-
- clean_range<-function(def,rng) {
- x1 <- rng[1]
- x2 <- rng[2]
- if (is.na(x1) || x1 == 0) x1 <- def[1]
- if (is.na(x2) || x2 == 0) x2 <- def[2]
- c(x1,x2)
- }
-
- get_ms2_leg <- m$aux$get_ms2_leg
-
- grouping <- m$conf$figures$grouping
- plot_group <- grouping$group
- plot_plot <- grouping$plot
- plot_ms1_label <- grouping$label
- plot_ms2_label <- "CE"
-
- doplot <- function(eic_ms1,eic_ms2,spec_ms2,leg_ms2,struct,group,plot,t_group="",t_plot="",print_labs=T) {
- ## Produce the filename.
- fn <- paste0(paste(t_group,group,t_plot,plot,sep = "_"),".pdf")
- fn <- gsub("\\[","",fn)
- fn <- gsub("\\]","",fn)
- fn <- gsub("\\+","p",fn)
- fn <- gsub("-","m",fn)
- fn <- if (!is.null(topdir)) file.path(topdir,fn) else fn
-
- ## Create an empty figure.
-
- xxdf <- eic_ms1$data[,.(rt=rt,intensity=intensity)]
- empty_fig <- ggplot2::ggplot(xxdf,ggplot2::aes(x=rt,y=intensity)) +
- ggplot2::geom_blank() +
- ggplot2::theme_void()
- leg1 <- cowplot::get_legend(eic_ms1)
- leg2 <- empty_fig
- if (NROW(eic_ms2$data) == 0)
- eic_ms2 <- empty_fig else {
- leg2 <- leg_ms2
- }
- if (NROW(spec_ms2$data) == 0) spec_ms2 <- empty_fig
- if (is.na(struct)) struct <- empty_fig
-
- ## Plot labels.
- labels <- if (print_labs) {
- c(paste0("EIC (MS1) ",t_group,": ",group,", ",t_plot,": ",plot),
- NA,
- paste0("EIC (MS2) ",t_group,": ",group,", ",t_plot,": ",plot),
- NA,
- paste0("MS2 Spectra ",t_group,": ",group,", ",t_plot,": ",plot),
- NA)
- } else {
- rep(NA,6)
-
- }
-
- ## Interval
- rt_int <- get_rt_interval(eic_ms1$data, eic_ms2$data, m$conf$figures)
- my_coord <- ggplot2::coord_cartesian(xlim = rt_int)
- big_fig <- cowplot::plot_grid(eic_ms1+my_coord+my_theme(),
- struct,
- eic_ms2+my_coord+my_theme(),
- leg2,
- spec_ms2 + my_theme(),
- leg1,
- align = "hv",
- axis='l',
- ncol = 2,
- nrow = 3,
- labels = labels,
- rel_widths = c(2,1))
-
- message("Saving plot: ",group,", ",plot," to ",fn)
- ggplot2::ggsave(plot=big_fig,width = 21, height = 29.7, units = "cm", filename = fn)
-
-
-
- }
-
-
- m$out$tab$ms2_plot[m$out$tab$ms1_plot,
- Map(function (ms1eic,
- ms2eic,
- ms2spec,
- leg,
- struct,
- grp,
- plt)
- doplot(ms1eic,ms2eic,ms2spec,
- leg,struct,grp,plt,
- t_group=m$conf$figures$grouping$group,
- t_plot=m$conf$figures$grouping$plot),
- i.fig_eic,
- x.fig_eic,
- x.fig_spec,
- x.fig_leg,
- i.fig_struct,
- .SD[[1]],
- .SD[[2]]),
- on=c(plot_group,plot_plot),
- .SDcols=c(plot_group,plot_plot)]
- m
-}
-
#' @export
report <- function(m) {
figtopdir <- FIG_TOPDIR #file.path(m$conf$project,FIG_TOPDIR)
--
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