| title |
output |
editor_options |
Locus Statistics |
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This will tabulate statistics per locus for presentation in a table.
library("tidyverse")
library("poppr")
load(file.path(PROJHOME, "data", "sclerotinia_16_loci.rda"))
dir.create(file.path(PROJHOME, "results", "tables"))makerange <- . %>% as.integer() %>% range() %>% paste(collapse = "--")
ranges <- map_chr(alleles(dat11), makerange)
# ranges <- c(ranges, alleles(dat11) %>% unlist(use.names = FALSE) %>% makerange)
locus_table(dat11, information = FALSE) %>%
as.data.frame() %>%
rownames_to_column("Locus") %>%
slice(-n()) %>%
mutate(Locus = gsub("\\([FH]\\)", "", Locus)) %>%
add_column(Range = ranges) %>%
add_column(Repeats = other(dat11)$REPLEN[locNames(dat11)]) %>%
select(Locus, Range, Repeats, allele, Hexp, Evenness) %>%
readr::write_csv(file.path(PROJHOME, "results/tables/locus-table.csv"), col_names = TRUE) %>%
mutate(allele = round(allele, 2)) %>%
mutate(Repeats = case_when(
Repeats <= 2 ~ "di-",
Repeats <= 3 ~ "tri-",
Repeats <= 4 ~ "tetra-",
Repeats <= 5 ~ "penta-",
Repeats <= 6 ~ "hexa-"
)) %>%
rename(`*h*` = Hexp) %>%
rename(`No. alleles` = allele) %>%
rename(`Repeat Motif` = Repeats) %>%
huxtable::as_huxtable(add_colnames = TRUE) %>%
huxtable::set_number_format(huxtable::everywhere, 3:4, 0) %>%
huxtable::set_number_format(huxtable::everywhere, 5:6, 2) %>%
huxtable::set_align(huxtable::everywhere, 2:6, "right") %>%
huxtable::set_col_width(c(0.06, 0.07, 0.11, 0.1, 0.05, 0.075)) %>%
huxtable::print_md(max_width = 61)-------------------------------------------------------
Locus Range Repeat Motif No. alleles *h* Evenness
------ -------- ------------ ----------- ---- ---------
5-2 318--324 di- 4 0.45 0.62
6-2 483--495 hexa- 3 0.64 0.95
7-2 158--174 di- 7 0.73 0.76
8-3 244--270 di- 7 0.74 0.79
9-2 360--382 di- 9 0.35 0.41
12-2 214--222 di- 5 0.58 0.78
17-3 342--363 tri- 7 0.55 0.53
20-3 280--282 di- 2 0.05 0.42
55-4 153--216 tetra- 10 0.72 0.66
110-4 370--386 tetra- 5 0.76 0.91
114-4 339--416 tetra- 10 0.83 0.80
-------------------------------------------------------
Session Information
## Session info --------------------------------------------------------------------------------------
## setting value
## version R version 3.4.2 (2017-09-28)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz UTC
## date 2018-04-12
## Packages ------------------------------------------------------------------------------------------
## package * version date source
## ade4 * 1.7-8 2017-08-09 cran (@1.7-8)
## adegenet * 2.1.0 2017-10-12 cran (@2.1.0)
## ape 5.0 2017-10-30 cran (@5.0)
## assertr 2.0.2.2 2017-06-06 cran (@2.0.2.2)
## assertthat 0.2.0 2017-04-11 CRAN (R 3.4.2)
## base * 3.4.2 2018-03-01 local
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## bindrcpp * 0.2 2017-06-17 CRAN (R 3.4.2)
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