From e9b91c6c05b85e65729b6dcd2d10daceb834c753 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Gularte=20M=C3=A9rida?= Date: Fri, 3 Mar 2023 13:31:20 -0500 Subject: [PATCH 1/3] Update plot-methods.R --- R/plot-methods.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/plot-methods.R b/R/plot-methods.R index b8a0186..1bd3cb0 100644 --- a/R/plot-methods.R +++ b/R/plot-methods.R @@ -40,6 +40,7 @@ setMethod("plot", signature(x="QDNAseqSignals", y="missing"), ampcol=getOption("QDNAseq::ampcol", "darkblue"), pointcol=getOption("QDNAseq::pointcol", "black"), segcol=getOption("QDNAseq::segcol", "chocolate"), + seglwd = 3, misscol=getOption("QDNAseq::misscol", NA), pointpch=getOption("QDNAseq::pointpch", 1L), pointcex=getOption("QDNAseq::pointcex", 0.1), @@ -240,7 +241,7 @@ setMethod("plot", signature(x="QDNAseqSignals", y="missing"), if (doSegments) { for (jjj in seq_len(nrow(segment))) { segments(pos[segment[jjj,2]], segment[jjj,1], - pos[segment[jjj,3]], segment[jjj,1], col=segcol, lwd=3) + pos[segment[jjj,3]], segment[jjj,1], col=segcol, lwd=seglwd) } } par(xpd=TRUE) From abf85765009b9464eedd974bb036bcbc9f964e38 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Gularte=20M=C3=A9rida?= Date: Fri, 3 Mar 2023 13:36:54 -0500 Subject: [PATCH 2/3] Update plot-methods.R --- R/plot-methods.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/plot-methods.R b/R/plot-methods.R index 1bd3cb0..9abbb55 100644 --- a/R/plot-methods.R +++ b/R/plot-methods.R @@ -40,7 +40,7 @@ setMethod("plot", signature(x="QDNAseqSignals", y="missing"), ampcol=getOption("QDNAseq::ampcol", "darkblue"), pointcol=getOption("QDNAseq::pointcol", "black"), segcol=getOption("QDNAseq::segcol", "chocolate"), - seglwd = 3, + seglwd = getOption("QDNAseq::segcol", 3), misscol=getOption("QDNAseq::misscol", NA), pointpch=getOption("QDNAseq::pointpch", 1L), pointcex=getOption("QDNAseq::pointcex", 0.1), From c3f21e906f7288464a90d3fa68d1fd00326143da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Rodrigo=20Gularte=20M=C3=A9rida?= Date: Fri, 3 Mar 2023 13:37:17 -0500 Subject: [PATCH 3/3] Update plot-methods.R --- R/plot-methods.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/plot-methods.R b/R/plot-methods.R index 9abbb55..9384ac5 100644 --- a/R/plot-methods.R +++ b/R/plot-methods.R @@ -40,7 +40,7 @@ setMethod("plot", signature(x="QDNAseqSignals", y="missing"), ampcol=getOption("QDNAseq::ampcol", "darkblue"), pointcol=getOption("QDNAseq::pointcol", "black"), segcol=getOption("QDNAseq::segcol", "chocolate"), - seglwd = getOption("QDNAseq::segcol", 3), + seglwd = getOption("QDNAseq::seglwd", 3), misscol=getOption("QDNAseq::misscol", NA), pointpch=getOption("QDNAseq::pointpch", 1L), pointcex=getOption("QDNAseq::pointcex", 0.1),