Merge pull request #640 from remlapmot/ggplot2-v4

TwoSampleMR 0.6.18 - fixes for ggplot2 version 4

Author: remlapmot

.github/workflows/check-full.yaml

@@ -28,7 +28,7 @@ jobs:
       # max-parallel: 2
       matrix:
         config:
-          - {os: macos-latest,   r: 'release'}
+          - {os: macos-15,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -37,8 +37,7 @@ jobs:
           - {os: ubuntu-latest,   r: '4.3.2'}
           - {os: ubuntu-latest,   r: 'oldrel-3'}
           - {os: ubuntu-latest,   r: 'oldrel-4'}
-          - {os: macos-15, r: 'release'}
-          - {os: macos-13, r: 'release'}
+          - {os: macos-14, r: 'release'}
           # - {os: ubuntu-24.04-arm, r: 'release', rspm: 'no' }
 
     env:

.gitignore

@@ -19,3 +19,9 @@ vignettes/*.html
 docs
 tests/testthat/*.pdf
 README.html
+vignettes/filename.pdf
+vignettes/filename.png
+vignettes/plot1.pdf
+vignettes/mr_report.md
+vignettes/figure/*.png
+vignettes/*.html

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.6.17
+Version: 0.6.18
 Authors@R: c(
     person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,10 @@
+# TwoSampleMR v0.6.18
+
+(Release date 2025-07-15)
+
+* Fixes to `mr_forest_plot()`, `forest_plot_1_to_many()`, `mr_leaveoneout_plot()`, and `mr_scatter_plot()` for compatibility with the forthcoming release of version 4 of **ggplot2**.
+* Made some minor improvements in the *Perform MR* vignette including adding back several of the forest plots.
+
 # TwoSampleMR v0.6.17
 
 (Release date 2025-06-22)

R/forest_plot2.R

@@ -131,13 +131,11 @@ format_mr_results <- function(mr_res, exponentiate=FALSE, single_snp_method="Wal
 
 	dat <- dat[order(dat$index), ]
 
-
 	dat <- dat[order(dat$outcome), ]
 
 	stopifnot(length(priority) == 1)
 
-	if(priority %in% dat$category)
-	{
+	if(priority %in% dat$category) {
 
 		temp1 <- subset(dat, category==priority)
 		temp2 <- subset(dat, category=="Other")
@@ -149,7 +147,6 @@ format_mr_results <- function(mr_res, exponentiate=FALSE, single_snp_method="Wal
 
 	}
 
-
 	return(dat)
 }
 
@@ -301,6 +298,7 @@ forest_plot_basic <- function(dat, section=NULL, colour_group=NULL, colour_group
 	dat <- merge(dat, l, by="lab", all.x=TRUE)
 	dat <- dat[rev(seq_len(nrow(dat))), ]
 
+	if (utils::packageVersion("ggplot2") <= "3.5.2") {
 	p <- ggplot2::ggplot(dat, ggplot2::aes(x=effect, y=exposure)) +
 	ggplot2::geom_rect(ggplot2::aes(fill=col), xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
 	ggplot2::geom_vline(xintercept=seq(ceiling(lo_orig), ceiling(up), by=0.5), colour="white", size=0.3) +
@@ -311,7 +309,7 @@ forest_plot_basic <- function(dat, section=NULL, colour_group=NULL, colour_group
 	ggplot2::facet_grid(lab ~ .) +
 	ggplot2::scale_x_continuous(trans=trans, limits=c(lo, up)) +
 	ggplot2::scale_colour_brewer(type="qual") +
-	ggplot2::scale_fill_manual(values=c("#eeeeee", "#ffffff"), guide=FALSE) +
+	ggplot2::scale_fill_manual(values=c("#eeeeee", "#ffffff"), guide="none") +
 	ggplot2::theme(
 		axis.line=ggplot2::element_blank(),
 		axis.text.y=ggplot2::element_blank(),
@@ -336,6 +334,43 @@ forest_plot_basic <- function(dat, section=NULL, colour_group=NULL, colour_group
 	) +
 	ggplot2::labs(y=NULL, x=xlabname, colour="", fill=NULL, title=main_title) +
 	outcome_labels
+	} else {
+	  p <- ggplot2::ggplot(dat, ggplot2::aes(x=effect, y=exposure)) +
+	    ggplot2::geom_rect(ggplot2::aes(fill=col), xmin=-Inf, xmax=Inf, ymin=-Inf, ymax=Inf) +
+	    ggplot2::geom_vline(xintercept=seq(ceiling(lo_orig), ceiling(up), by=0.5), colour="white", size=0.3) +
+	    ggplot2::geom_vline(xintercept=null_line, colour="#333333", size=0.3) +
+	    ggplot2::geom_errorbarh(ggplot2::aes(xmin=lo_ci, xmax=up_ci), width=0, size=0.4, colour="#aaaaaa") +
+	    ggplot2::geom_point(colour="black", size=2.2) +
+	    point_plot +
+	    ggplot2::facet_grid(lab ~ .) +
+	    ggplot2::scale_x_continuous(trans=trans, limits=c(lo, up)) +
+	    ggplot2::scale_colour_brewer(type="qual") +
+	    ggplot2::scale_fill_manual(values=c("#eeeeee", "#ffffff"), guide="none") +
+	    ggplot2::theme(
+	      axis.line=ggplot2::element_blank(),
+	      axis.text.y=ggplot2::element_blank(),
+	      axis.ticks.y=ggplot2::element_blank(),
+	      axis.text.x=text_colour,
+	      axis.ticks.x=tick_colour,
+	      # strip.text.y=ggplot2::element_text(angle=360, hjust=0),
+	      strip.background=ggplot2::element_rect(fill="white", colour="white"),
+	      strip.text=ggplot2::element_text(family="Courier New", face="bold", size=9),
+	      legend.position="none",
+	      legend.direction="vertical",
+	      panel.grid.minor.x=ggplot2::element_blank(),
+	      panel.grid.minor.y=ggplot2::element_blank(),
+	      panel.grid.major.y=ggplot2::element_blank(),
+	      plot.title = ggplot2::element_text(hjust = 0, size=12, colour=title_colour),
+	      plot.margin=ggplot2::unit(c(2,3,2,0), units="points"),
+	      plot.background=ggplot2::element_rect(fill="white"),
+	      panel.spacing=ggplot2::unit(0,"lines"),
+	      panel.background=ggplot2::element_rect(colour="red", fill="grey", size=1),
+	      strip.text.y = ggplot2::element_blank()
+	      # strip.background = ggplot2::element_blank()
+	    ) +
+	    ggplot2::labs(y=NULL, x=xlabname, colour="", fill=NULL, title=main_title) +
+	    outcome_labels
+	}
 	return(p)
 }
 
@@ -401,7 +436,7 @@ forest_plot_names <- function(dat, section=NULL, bottom=TRUE)
 	ggplot2::facet_grid(lab ~ .) +
 	ggplot2::scale_x_continuous(limits=c(lo, up)) +
 	ggplot2::scale_colour_brewer(type="qual") +
-	ggplot2::scale_fill_manual(values=c("#eeeeee", "#ffffff"), guide=FALSE) +
+	ggplot2::scale_fill_manual(values=c("#eeeeee", "#ffffff"), guide="none") +
 	ggplot2::theme(
 		axis.line=ggplot2::element_blank(),
 		axis.text.y=ggplot2::element_blank(),
@@ -485,10 +520,8 @@ forest_plot <- function(mr_res, exponentiate=FALSE, single_snp_method="Wald rati
 		ggplot2::theme(text=ggplot2::element_text(size=10))
 	)
 
-	if(!by_category)
-	{
-		if(!in_columns)
-		{
+	if(!by_category) {
+		if(!in_columns) {
 			return(forest_plot_basic(
 				dat,
 				bottom = TRUE,
@@ -506,8 +539,7 @@ forest_plot <- function(mr_res, exponentiate=FALSE, single_snp_method="Wald rati
 			)
 			count <- 2
 			columns <- unique(dat$exposure)
-			for(i in seq_along(columns))
-			{
+			for(i in seq_along(columns)) {
 				l[[count]] <- forest_plot_basic(
 					dat,
 					section=NULL,
@@ -534,13 +566,11 @@ forest_plot <- function(mr_res, exponentiate=FALSE, single_snp_method="Wald rati
 		}
 	}
 
-	if(!in_columns)
-	{
+	if(!in_columns) {
 		sec <- unique(as.character(dat$category))
 		h <- rep(0, length(sec))
 		l <- list()
-		for(i in seq_along(sec))
-		{
+		for(i in seq_along(sec)) {
 			l[[i]] <- forest_plot_basic(
 				dat,
 				sec[i],
@@ -570,17 +600,15 @@ forest_plot <- function(mr_res, exponentiate=FALSE, single_snp_method="Wald rati
 		l <- list()
 		h <- rep(0, length(sec))
 		count <- 1
-		for(i in seq_along(sec))
-		{
+		for(i in seq_along(sec)) {
 			h[i] <- length(unique(subset(dat, category==sec[i])$outcome))
 			l[[count]] <- forest_plot_names(
 				dat,
 				sec[i],
 				bottom = i==length(sec)
 			)
 			count <- count + 1
-			for(j in seq_along(columns))
-			{
+			for(j in seq_along(columns)) {
 				l[[count]] <- forest_plot_basic(
 					dat,
 					sec[i],