air format R/scatterplot.R

Author: remlapmot

R/scatterplot.R

@@ -6,52 +6,104 @@
 #' @param dat Output from [harmonise_data()].
 #' @export
 #' @return List of plots
-mr_scatter_plot <- function(mr_results, dat)
-{
-	# dat <- subset(dat, paste(id.outcome, id.exposure) %in% paste(mr_results$id.outcome, mr_results$id.exposure))
-	mrres <- plyr::dlply(dat, c("id.exposure", "id.outcome"), function(d)
-	{
-		d <- plyr::mutate(d)
-		if(nrow(d) < 2 | sum(d$mr_keep) == 0)
-		{
-			return(blank_plot("Insufficient number of SNPs"))
-		}
-		d <- subset(d, mr_keep)
-		index <- d$beta.exposure < 0
-		d$beta.exposure[index] <- d$beta.exposure[index] * -1
-		d$beta.outcome[index] <- d$beta.outcome[index] * -1
-		mrres <- subset(mr_results, id.exposure == d$id.exposure[1] & id.outcome == d$id.outcome[1])
-		mrres$a <- 0
-		if("MR Egger" %in% mrres$method)
-		{
-			temp <- mr_egger_regression(d$beta.exposure, d$beta.outcome, d$se.exposure, d$se.outcome, default_parameters())
-			mrres$a[mrres$method == "MR Egger"] <- temp$b_i
-		}
+mr_scatter_plot <- function(mr_results, dat) {
+  # dat <- subset(dat, paste(id.outcome, id.exposure) %in% paste(mr_results$id.outcome, mr_results$id.exposure))
+  mrres <- plyr::dlply(dat, c("id.exposure", "id.outcome"), function(d) {
+    d <- plyr::mutate(d)
+    if (nrow(d) < 2 | sum(d$mr_keep) == 0) {
+      return(blank_plot("Insufficient number of SNPs"))
+    }
+    d <- subset(d, mr_keep)
+    index <- d$beta.exposure < 0
+    d$beta.exposure[index] <- d$beta.exposure[index] * -1
+    d$beta.outcome[index] <- d$beta.outcome[index] * -1
+    mrres <- subset(
+      mr_results,
+      id.exposure == d$id.exposure[1] & id.outcome == d$id.outcome[1]
+    )
+    mrres$a <- 0
+    if ("MR Egger" %in% mrres$method) {
+      temp <- mr_egger_regression(
+        d$beta.exposure,
+        d$beta.outcome,
+        d$se.exposure,
+        d$se.outcome,
+        default_parameters()
+      )
+      mrres$a[mrres$method == "MR Egger"] <- temp$b_i
+    }
 
-		if("MR Egger (bootstrap)" %in% mrres$method)
-		{
-			temp <- mr_egger_regression_bootstrap(d$beta.exposure, d$beta.outcome, d$se.exposure, d$se.outcome, default_parameters())
-			mrres$a[mrres$method == "MR Egger (bootstrap)"] <- temp$b_i
-		}
+    if ("MR Egger (bootstrap)" %in% mrres$method) {
+      temp <- mr_egger_regression_bootstrap(
+        d$beta.exposure,
+        d$beta.outcome,
+        d$se.exposure,
+        d$se.outcome,
+        default_parameters()
+      )
+      mrres$a[mrres$method == "MR Egger (bootstrap)"] <- temp$b_i
+    }
 
-		ggplot2::ggplot(data=d, ggplot2::aes(x=beta.exposure, y=beta.outcome)) +
-			ggplot2::geom_errorbar(ggplot2::aes(ymin=beta.outcome-se.outcome, ymax=beta.outcome+se.outcome), colour="grey", width=0) +
-			ggplot2::geom_errorbarh(ggplot2::aes(xmin=beta.exposure-se.exposure, xmax=beta.exposure+se.exposure), colour="grey", height=0) +
-			ggplot2::geom_point() +
-			ggplot2::geom_abline(data=mrres, ggplot2::aes(intercept=a, slope=b, colour=method), show.legend=TRUE) +
-			ggplot2::scale_colour_manual(values=c("#a6cee3", "#1f78b4", "#b2df8a", "#33a02c", "#fb9a99", "#e31a1c", "#fdbf6f", "#ff7f00", "#cab2d6", "#6a3d9a", "#ffff99", "#b15928")) +
-			ggplot2::labs(colour="MR Test", x=paste("SNP effect on", d$exposure[1]), y=paste("SNP effect on", d$outcome[1])) +
-			ggplot2::theme(legend.position="top", legend.direction="vertical") +
-			ggplot2::guides(colour=ggplot2::guide_legend(ncol=2))
-	})
-	mrres
+    ggplot2::ggplot(
+      data = d,
+      ggplot2::aes(x = beta.exposure, y = beta.outcome)
+    ) +
+      ggplot2::geom_errorbar(
+        ggplot2::aes(
+          ymin = beta.outcome - se.outcome,
+          ymax = beta.outcome + se.outcome
+        ),
+        colour = "grey",
+        width = 0
+      ) +
+      ggplot2::geom_errorbarh(
+        ggplot2::aes(
+          xmin = beta.exposure - se.exposure,
+          xmax = beta.exposure + se.exposure
+        ),
+        colour = "grey",
+        height = 0
+      ) +
+      ggplot2::geom_point() +
+      ggplot2::geom_abline(
+        data = mrres,
+        ggplot2::aes(intercept = a, slope = b, colour = method),
+        show.legend = TRUE
+      ) +
+      ggplot2::scale_colour_manual(
+        values = c(
+          "#a6cee3",
+          "#1f78b4",
+          "#b2df8a",
+          "#33a02c",
+          "#fb9a99",
+          "#e31a1c",
+          "#fdbf6f",
+          "#ff7f00",
+          "#cab2d6",
+          "#6a3d9a",
+          "#ffff99",
+          "#b15928"
+        )
+      ) +
+      ggplot2::labs(
+        colour = "MR Test",
+        x = paste("SNP effect on", d$exposure[1]),
+        y = paste("SNP effect on", d$outcome[1])
+      ) +
+      ggplot2::theme(legend.position = "top", legend.direction = "vertical") +
+      ggplot2::guides(colour = ggplot2::guide_legend(ncol = 2))
+  })
+  mrres
 }
 
 
-blank_plot <- function(message)
-{
-	ggplot2::ggplot(data.frame(a=0,b=0,n=message)) +
-    ggplot2::geom_text(ggplot2::aes(x=a,y=b,label=n)) +
-    ggplot2::labs(x=NULL,y=NULL) +
-    ggplot2::theme(axis.text=ggplot2::element_blank(), axis.ticks=ggplot2::element_blank())
+blank_plot <- function(message) {
+  ggplot2::ggplot(data.frame(a = 0, b = 0, n = message)) +
+    ggplot2::geom_text(ggplot2::aes(x = a, y = b, label = n)) +
+    ggplot2::labs(x = NULL, y = NULL) +
+    ggplot2::theme(
+      axis.text = ggplot2::element_blank(),
+      axis.ticks = ggplot2::element_blank()
+    )
 }