Merge pull request #638 from remlapmot/v0-6-17

remlapmot · web-flow · commit a62018f820c5 · 2025-06-22T11:41:15.000+01:00
TwoSampleMR 0.6.17
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TwoSampleMR
 Title: Two Sample MR Functions and Interface to MRC Integrative
     Epidemiology Unit OpenGWAS Database
-Version: 0.6.16
+Version: 0.6.17
 Authors@R: c(
     person("Gibran", "Hemani", , "g.hemani@bristol.ac.uk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0920-1055")),
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# TwoSampleMR v0.6.17
+
+(Release date 2025-06-22)
+
+* Continued amends to the plot for MR-GRIP (thanks @fdudbridge)
+
 # TwoSampleMR v0.6.16
 
 (Release date 2025-06-05)
diff --git a/R/scatterplot.R b/R/scatterplot.R
@@ -52,10 +52,7 @@ mr_scatter_plot <- function(mr_results, dat) {
         d$se.outcome,
         default_parameters()
       )
-      # keep intercept at 0 because plot on gd versus gp axes
-      # mrres$a[mrres$method == "MR GRIP"] <- temp$b_i
-      msgtxt <- paste0("Strictly, it is only valid to view the MR-GRIP estimate on the standard MR scatter plot axes when the intercept is zero. The estimated intercept for this model is: ", signif(temp$b_i))
-      message(msgtxt)
+      mrres$a[mrres$method == "MR GRIP"] <- stats::lm(d$beta.outcome - temp$b*d$beta.exposure ~ 1, weights = 1/d$se.outcome^2)$coef
     }
 
     ggplot2::ggplot(

Original file line number	Diff line number	Diff line change
`@@ -52,10 +52,7 @@ mr_scatter_plot <- function(mr_results, dat) {`
`52`	`52`	`d$se.outcome,`
`53`	`53`	`default_parameters()`
`54`	`54`	`)`
`55`		`- # keep intercept at 0 because plot on gd versus gp axes`
`56`		`- # mrres$a[mrres$method == "MR GRIP"] <- temp$b_i`
`57`		`- msgtxt <- paste0("Strictly, it is only valid to view the MR-GRIP estimate on the standard MR scatter plot axes when the intercept is zero. The estimated intercept for this model is: ", signif(temp$b_i))`
`58`		`- message(msgtxt)`
	`55`	`+ mrres$a[mrres$method == "MR GRIP"] <- stats::lm(d$beta.outcome - temp$b*d$beta.exposure ~ 1, weights = 1/d$se.outcome^2)$coef`
`59`	`56`	`}`
`60`	`57`
`61`	`58`	`ggplot2::ggplot(`