Merge pull request #642 from remlapmot/ggplot2-v4-2

TwoSampleMR 0.6.19

Author: remlapmot

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.6.18
+Version: 0.6.19
 Authors@R: c(
     person("Gibran", "Hemani", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),

NEWS.md

@@ -1,3 +1,9 @@
+# TwoSampleMR v0.6.19
+
+(Release date 2025-07-21)
+
+* Further fixes for the forthcoming version 4 of ggplot2.
+
 # TwoSampleMR v0.6.18
 
 (Release date 2025-07-15)

R/forest_plot2.R

@@ -339,7 +339,7 @@ forest_plot_basic <- function(dat, section=NULL, colour_group=NULL, colour_group
 	    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_errorbar(ggplot2::aes(xmin=lo_ci, xmax=up_ci), width=0, size=0.4, colour="#aaaaaa", orientation = "y") +
 	    ggplot2::geom_point(colour="black", size=2.2) +
 	    point_plot +
 	    ggplot2::facet_grid(lab ~ .) +

R/forest_plot_1-to-many.R

@@ -346,7 +346,7 @@ forest_plot_basic2 <- function(dat, section=NULL, colour_group=NULL, colour_grou
 	    ggplot2::geom_vline(xintercept=seq(ceiling(lo_orig), ceiling(up), by=0.5), alpha=0, linewidth=0.3) +
 	    ggplot2::geom_vline(xintercept=null_line, colour="#333333", linewidth=0.3) +
 	    # ggplot2::geom_errorbarh(ggplot2::aes(xmin=lo_ci, xmax=up_ci), height=0, size=0.4, colour="#aaaaaa") +
-	    ggplot2::geom_errorbarh(ggplot2::aes(xmin=lo_ci, xmax=up_ci), width=0, linewidth=0.4, colour=colour_scheme) +
+	    ggplot2::geom_errorbar(ggplot2::aes(xmin=lo_ci, xmax=up_ci), width=0, linewidth=0.4, colour=colour_scheme, orientation = "y") +
 	    # ggplot2::geom_point(colour="black", size=2.2) +
 	    ggplot2::geom_point(colour=colour_scheme, size=2.2,shape=shape_points,fill=colour_scheme) +
 	    # ggplot2::scale_fill_manual(values="cyan4")+

R/leaveoneout.R

@@ -129,7 +129,7 @@ mr_leaveoneout_plot <- function(leaveoneout_results)
 		  ggplot2::ggplot(d, ggplot2::aes(y=SNP, x=b)) +
 		    ggplot2::geom_vline(xintercept=0, linetype="dotted") +
 		    # ggplot2::geom_errorbarh(ggplot2::aes(xmin=pmax(lo, min(d$b, na.rm=T)), xmax=pmin(up, max(d$b, na.rm=T)), size=as.factor(tot), colour=as.factor(tot)), height=0) +
-		    ggplot2::geom_errorbarh(ggplot2::aes(xmin=lo, xmax=up, linewidth=as.factor(tot), colour=as.factor(tot)), width=0) +
+		    ggplot2::geom_errorbar(ggplot2::aes(xmin=lo, xmax=up, linewidth=as.factor(tot), colour=as.factor(tot)), width=0, orientation = "y") +
 		    ggplot2::geom_point(ggplot2::aes(colour=as.factor(tot))) +
 		    ggplot2::geom_hline(ggplot2::aes(yintercept = which(levels(SNP) %in% "")), colour="grey") +
 		    ggplot2::scale_colour_manual(values=c("black", "red")) +

R/scatterplot.R

@@ -118,13 +118,14 @@ mr_scatter_plot <- function(mr_results, dat) {
           colour = "grey",
           width = 0
         ) +
-        ggplot2::geom_errorbarh(
+        ggplot2::geom_errorbar(
           ggplot2::aes(
             xmin = beta.exposure - se.exposure,
             xmax = beta.exposure + se.exposure
           ),
           colour = "grey",
-          width = 0
+          width = 0,
+          orientation = "y"
         ) +
         ggplot2::geom_point() +
         ggplot2::geom_abline(

R/singlesnp.R

@@ -131,7 +131,7 @@ mr_forest_plot <- function(singlesnp_results, exponentiate=FALSE)
 		  ggplot2::ggplot(d, ggplot2::aes(y=SNP, x=b)) +
 		    ggplot2::geom_vline(xintercept=xint, linetype="dotted") +
 		    # ggplot2::geom_errorbarh(ggplot2::aes(xmin=pmax(lo, min(d$b, na.rm=T)), xmax=pmin(up, max(d$b, na.rm=T)), size=as.factor(tot), colour=as.factor(tot)), height=0) +
-		    ggplot2::geom_errorbarh(ggplot2::aes(xmin=lo, xmax=up, linewidth=as.factor(tot), colour=as.factor(tot)), width=0) +
+		    ggplot2::geom_errorbar(ggplot2::aes(xmin=lo, xmax=up, linewidth=as.factor(tot), colour=as.factor(tot)), width=0, orientation = "y") +
 		    ggplot2::geom_point(ggplot2::aes(colour=as.factor(tot))) +
 		    ggplot2::geom_hline(ggplot2::aes(yintercept = which(levels(SNP) %in% "")), colour="grey") +
 		    ggplot2::scale_colour_manual(values=c("black", "red")) +

tests/testthat/test_plots.R

@@ -74,7 +74,7 @@ test_that("Forest plot 1 to many", {
 
 test_that("Forest plot 1 to many test 2", {
   res$pval<-formatC(res$pval, format = "e", digits = 2)
-  expect_warning(p9 <- utils::capture.output(forest_plot_1_to_many(
+  expect_warning(utils::capture.output(p9 <- forest_plot_1_to_many(
     res,
     b = "b",
     se = "se",