Closed siberianhigh closed 4 years ago
That's not normal. thanks for highlighting the bug, will have a look at it today.
Great, I ready to provide data files used, if necessary. But I got these problems with different vcf/metadata combinations.
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
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: ColumnPOP2
has different attributes on LHS and RHS of join─ Packages package version date lib source
ade4 1.7-13 2018-08-31 [1] CRAN (R 3.6.1)
adegenet 2.1.1 2018-02-02 [1] CRAN (R 3.6.1)
ape 5.3 2019-03-17 [1] CRAN (R 3.6.1)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
assigner 0.5.6 2019-12-08 [1] Github (thierrygosselin/assigner@b941111) backports 1.1.5 2019-10-02 [1] CRAN (R 3.6.1)
Biobase 2.44.0 2019-05-02 [1] Bioconductor
BiocGenerics 0.30.0 2019-05-02 [1] Bioconductor
Biostrings 2.52.0 2019-05-02 [1] Bioconductor
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.1)
boot 1.3-24 2019-12-20 [4] CRAN (R 3.6.2)
broom 0.5.2 2019-04-07 [1] CRAN (R 3.6.1)
callr 3.3.2 2019-09-22 [1] CRAN (R 3.6.1)
class 7.3-15 2019-01-01 [4] CRAN (R 3.6.1)
classInt 0.4-2 2019-10-17 [1] CRAN (R 3.6.1)
cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
cluster 2.1.0 2019-06-19 [4] CRAN (R 3.6.1)
coda 0.19-3 2019-07-05 [1] CRAN (R 3.6.1)
colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.1)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
data.table 1.12.6 2019-10-18 [1] CRAN (R 3.6.1)
DBI 1.0.0 2018-05-02 [1] CRAN (R 3.6.1)
deldir 0.1-23 2019-07-31 [1] CRAN (R 3.6.1)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.1.0 2019-07-06 [1] CRAN (R 3.6.1)
digest 0.6.23 2019-11-23 [1] CRAN (R 3.6.1)
dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.1)
e1071 1.7-3 2019-11-26 [1] CRAN (R 3.6.1)
ellipsis 0.3.0 2019-09-20 [1] CRAN (R 3.6.1)
expm 0.999-4 2019-03-21 [1] CRAN (R 3.6.1)
fansi 0.4.0 2018-10-05 [1] CRAN (R 3.6.1)
farver 2.0.1 2019-11-13 [1] CRAN (R 3.6.1)
fastmap 1.0.1 2019-10-08 [1] CRAN (R 3.6.1)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
fst 0.9.0 2019-04-09 [1] CRAN (R 3.6.1)
gdata 2.18.0 2017-06-06 [1] CRAN (R 3.6.1)
gdsfmt 1.20.0 2019-05-02 [1] Bioconductor
generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
GenomeInfoDb 1.20.0 2019-05-02 [1] Bioconductor
GenomeInfoDbData 1.2.1 2019-12-08 [1] Bioconductor
GenomicRanges 1.36.1 2019-09-06 [1] Bioconductor
ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.1)
glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
gmodels 2.18.1 2018-06-25 [1] CRAN (R 3.6.1)
gridExtra 2.3 2017-09-09 [1] CRAN (R 3.6.1)
gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.1)
gtools 3.8.1 2018-06-26 [1] CRAN (R 3.6.1)
GWASExactHW 1.01 2013-01-05 [1] CRAN (R 3.6.1)
hms 0.5.2 2019-10-30 [1] CRAN (R 3.6.1)
htmltools 0.4.0 2019-10-04 [1] CRAN (R 3.6.1)
httpuv 1.5.2 2019-09-11 [1] CRAN (R 3.6.1)
igraph 1.2.4.2 2019-11-27 [1] CRAN (R 3.6.1)
IRanges 2.18.3 2019-09-24 [1] Bioconductor
jomo 2.6-10 2019-10-22 [1] CRAN (R 3.6.1)
KernSmooth 2.23-16 2019-10-15 [4] CRAN (R 3.6.1)
labeling 0.3 2014-08-23 [1] CRAN (R 3.6.1)
later 1.0.0 2019-10-04 [1] CRAN (R 3.6.1)
lattice 0.20-38 2018-11-04 [4] CRAN (R 3.6.1)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.1)
LearnBayes 2.15.1 2018-03-18 [1] CRAN (R 3.6.1)
lifecycle 0.1.0 2019-08-01 [1] CRAN (R 3.6.1)
lme4 1.1-21 2019-03-05 [1] CRAN (R 3.6.1)
logistf 1.23 2018-07-19 [1] CRAN (R 3.6.1)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
MASS 7.3-51.5 2019-12-20 [4] CRAN (R 3.6.2)
Matrix 1.2-18 2019-11-27 [4] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
mgcv 1.8-31 2019-11-09 [4] CRAN (R 3.6.1)
mice 3.6.0 2019-07-10 [1] CRAN (R 3.6.1)
mime 0.7 2019-06-11 [1] CRAN (R 3.6.1)
minqa 1.2.4 2014-10-09 [1] CRAN (R 3.6.1)
mitml 0.3-7 2019-01-07 [1] CRAN (R 3.6.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.1)
nlme 3.1-143 2019-12-10 [4] CRAN (R 3.6.2)
nloptr 1.2.1 2018-10-03 [1] CRAN (R 3.6.1)
nnet 7.3-12 2016-02-02 [4] CRAN (R 3.6.1)
pan 1.6 2018-06-29 [1] CRAN (R 3.6.1)
pbmcapply 1.5.0 2019-07-10 [1] CRAN (R 3.6.1)
permute 0.9-5 2019-03-12 [1] CRAN (R 3.6.1)
pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.1)
pinfsc50 1.1.0 2016-12-02 [1] CRAN (R 3.6.1)
pkgbuild 1.0.5 2019-08-26 [1] CRAN (R 3.6.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.1)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
promises 1.1.0 2019-10-04 [1] CRAN (R 3.6.1)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
purrr 0.3.3 2019-10-18 [1] CRAN (R 3.6.1)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.1)
radiator 1.1.2 2019-12-08 [1] Github (thierrygosselin/radiator@480ef0f) Rcpp 1.0.3 2019-11-08 [1] CRAN (R 3.6.1)
RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.1)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.1)
rlang 0.4.2 2019-11-23 [1] CRAN (R 3.6.1)
rpart 4.1-15 2019-04-12 [4] CRAN (R 3.6.1)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.1)
S4Vectors 0.22.1 2019-09-09 [1] Bioconductor
scales 1.1.0 2019-11-18 [1] CRAN (R 3.6.1)
SeqArray 1.24.2 2019-07-12 [1] Bioconductor
seqinr 3.6-1 2019-09-07 [1] CRAN (R 3.6.1)
SeqVarTools 1.22.0 2019-05-02 [1] Bioconductor
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
sf 0.8-0 2019-09-17 [1] CRAN (R 3.6.1)
shiny 1.4.0 2019-10-10 [1] CRAN (R 3.6.1)
sp 1.3-2 2019-11-07 [1] CRAN (R 3.6.1)
spData 0.3.2 2019-09-19 [1] CRAN (R 3.6.1)
spdep 1.1-3 2019-09-18 [1] CRAN (R 3.6.1)
stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.1)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
survival 3.1-8 2019-12-03 [4] CRAN (R 3.6.2)
testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.1)
tidyr 1.0.0 2019-09-11 [1] CRAN (R 3.6.1)
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usethis 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
utf8 1.1.4 2018-05-24 [1] CRAN (R 3.6.1)
vcfR 1.8.0 2018-04-17 [1] CRAN (R 3.6.1)
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vegan 2.5-6 2019-09-01 [1] CRAN (R 3.6.1)
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zlibbioc 1.30.0 2019-05-02 [1] Bioconductor