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thierrygosselin / assigner

Population assignment analysis using R
http://thierrygosselin.github.io/assigner
GNU General Public License v3.0
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digits in heatmap_fst() #17

Closed siberianhigh closed 4 years ago

siberianhigh commented 4 years ago

Nothing happens when I'm trying to change argument 'digits' in heatmap_fst(), it is always 5 decimal digits on heatmap. For instance:

heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE, digits = 3, color.low = "white", color.mid = "grey", color.high = "black", text.size = 4, plot.size = 40, pop.levels = NULL, path.folder = NULL, filename = NULL)

heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE, digits = 5, color.low = "white", color.mid = "grey", color.high = "black", text.size = 4, plot.size = 40, pop.levels = NULL, path.folder = NULL, filename = NULL)

heatmap_fst(fst.ci$pairwise.fst.full.matrix, fst.ci$pairwise.fst.ci.matrix, n.s = TRUE, digits = 8, color.low = "white", color.mid = "grey", color.high = "black", text.size = 4, plot.size = 40, pop.levels = NULL, path.folder = NULL, filename = NULL)

all three give me identical results.

There is another problem, probably related to the described above - the fst values and corresponding CI intervals are mixed between upper and lower parts of matrix on the heatmap:

Warning messages: 1: Column POP1 has different attributes on LHS and RHS of join 2: Column POP2 has different attributes on LHS and RHS of join

plot

devtools::session_info() ─ Session info setting value
version R version 3.6.2 (2019-12-12) os Ubuntu 18.04.3 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Asia/Yekaterinburg
date 2020-01-07

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thierrygosselin commented 4 years ago

That's not normal. thanks for highlighting the bug, will have a look at it today.

siberianhigh commented 4 years ago

Great, I ready to provide data files used, if necessary. But I got these problems with different vcf/metadata combinations.

thierrygosselin commented 4 years ago

problem 1: digits

solved. it was fixed internally

problem 2: Fst and CI mixed up

This was caused by pop.levels = NULL. When this argument is supplied a string, it works Now when NULL the info is taken from the Fst data file/object column names. Documentation was updated.

Remember that you can generate the heatmap as you do the Fst using ... argument.

Cheers and thanks for highlighting the bug

v. 0.5.7 fixes the problems