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bcm-uga / Loter

A software package for local ancestry inference and haplotype phasing
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Plotting of output #23

Closed DEYANGEIOZ closed 1 year ago

DEYANGEIOZ commented 2 years ago

Hi, Thank you very much for your great contribution on this. Is there a simple way to plot the result in R, and to generate vector files that could be compiled in the following step? I found it is different from the common heatmap structure. Thank you.
Deyan

gdurif commented 2 years ago

Hi, Could give me more details about what you want to do with the results ? You could use the option -f txt for loter_cli which will produce a text data file with individuals in rows and inferred ancestry in columns. Then, you can load this result file within R (e.f. with read.table) and plot the result in R with

res <- read.table(...)
heatmap(res, Rowv = NA, Colv = NA, scale = "none")

Do not hesitate if you have any further question. Best