[adegenet-forum] glPlot: which sample is used as the reference?

Jombart, Thibaut t.jombart at imperial.ac.uk
Tue Jan 13 18:58:18 CET 2015

Hi there,
individuals are plotted according to their order in the genlight object (individuals' indices are indicated on the y-axis.

From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Yan Hou [yan.hou at nhm.uio.no]
Sent: 12 January 2015 21:26
To: adegenet-forum at lists.r-forge.r-project.org
Cc: Yan Hou
Subject: [adegenet-forum] glPlot: which sample is used as the reference?

I managed to use glPlot( SNPs,posi="topleft" ) to present the position of SNPs in my concatenated and aligned RAD-seq data matrix. When looking at the figure, I wonder which sample was used as the reference? The first sample in the input file or the sample with most complete sequence data? My first sample has a large number of missing data, so I wonder?


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