Nothing
## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(comment = ">", fig.align = 'center', fig.height = 4.5, fig.width = 4.5, fig.show = "hold")
## ----echo = FALSE, fig.height = 3, fig.width = 3------------------------------
oldpar = par(mar = rep(0.1, 4))
plot.new()
seq = c(
"AACTCAGACGA",
"AAGCGACAACT",
"ACGTCACACCA",
"AACCCAGCACT",
"AAGCCGGACCA",
"AAGCCGGACCA",
"GAGCCGGACCT",
"AAGCCGGACCT"
)
for (i in seq_along(seq)) {
n = strsplit(seq[i], "")[[1]]
text(((0:10) + 0.5) / 11, (8 - i) / 8 + 1 / 16, n)
}
transparent_red <- adjustcolor("red", alpha.f = 0.5)
transparent_blue <- adjustcolor("blue", alpha.f = 0.5)
polygon(
c(0, 11, 11, 0, 0, 1, 1, 0, 0) / 11,
c(4, 4, 0, 0, 1, 1, 2, 2, 4) / 8,
border = transparent_red,
col = transparent_red
)
polygon(
c(3, 7, 7, 8, 8, 7, 7, 4, 4, 3, 3, 5, 5, 3) / 11,
c(8, 8, 7, 7, 5, 5, 4, 4, 5, 5, 6, 6, 7, 7) / 8,
border = transparent_blue,
col = transparent_blue
)
polygon(c(5, 6, 6, 5) / 11, c(8, 8, 0, 0) / 8, border = "black")
par(oldpar)
## ----library, message = FALSE-------------------------------------------------
library(rehh)
## -----------------------------------------------------------------------------
make.example.files()
## -----------------------------------------------------------------------------
cat(readLines("example1.hap"), sep = "\n")
## -----------------------------------------------------------------------------
cat(readLines("example1.map"), sep = "\n")
## -----------------------------------------------------------------------------
cat(readLines("example1.vcf"), sep = "\n")
## -----------------------------------------------------------------------------
hh <- data2haplohh(hap_file = "example1.hap",
map_file = "example1.map",
allele_coding = "01")
## -----------------------------------------------------------------------------
hh_map <- data2haplohh(hap_file = "example1.hap",
map_file = "example1.map",
allele_coding = "map",
verbose = FALSE)
identical(hh, hh_map)
hh_none <- data2haplohh(hap_file = "example1.hap",
map_file = "example1.map",
allele_coding = "none",
verbose = FALSE)
identical(hh, hh_none)
## ---- eval = requireNamespace("data.table", quietly = TRUE)-------------------
hh_vcf <- data2haplohh(hap_file = "example1.vcf",
vcf_reader = "data.table",
verbose = FALSE)
identical(hh, hh_vcf)
## ----hhplot1, fig.cap = "Graphical output of the plot.haplohh() function"-----
plot(hh)
## -----------------------------------------------------------------------------
res <- calc_ehh(hh, mrk = "rs6", include_nhaplo = TRUE)
res
## -----------------------------------------------------------------------------
haplo(hh)
## ----ehh, fig.align = 'center', fig.cap = "Graphical output of the plot.ehh() function", fig.pos = '!h', fig.lp = 'fig:'----
plot(res)
## -----------------------------------------------------------------------------
res <- calc_ehh(hh,
mrk = "rs6",
include_nhaplo = TRUE,
phased = FALSE)
res
## ----ehhunphased, fig.align = 'center', fig.cap = "Graphical output of the plot.ehh() function", fig.pos = '!h', fig.lp = 'fig:'----
plot(res)
## -----------------------------------------------------------------------------
res <- calc_ehhs(hh,
mrk = "rs6",
include_nhaplo = TRUE,
discard_integration_at_border = FALSE)
res
## ----ehhs1, fig.align = 'center', fig.cap = "Graphical output of the plot.ehhs() function", fig.pos = '!h', fig.lp = 'fig:'----
plot(res)
## -----------------------------------------------------------------------------
res.scan <- scan_hh(hh, discard_integration_at_border = FALSE)
res.scan
## -----------------------------------------------------------------------------
ihs <- ihh2ihs(res.scan, freqbin = 1, verbose = FALSE)
ihs
## -----------------------------------------------------------------------------
cr <- calc_candidate_regions(ihs, threshold = 1.5, ignore_sign = TRUE, window_size = 1)
cr
## ----manhattan11, fig.align = 'center', fig.cap = "Graphical output of the manhattanplot() function", fig.pos = '!h', fig.lp = 'fig:'----
manhattanplot(ihs, threshold = c(-1.5,1.5), cr = cr, ylim = c(-2.5,2.5), pch = 20)
## ----furcation11, fig.cap = "Graphical output of the plot.furcation() function", fig.pos = '!h', fig.lp = 'fig:'----
f <- calc_furcation(hh, mrk = "rs6")
# set equal plot margins on left and right side and save old ones
oldpar <- par(mar = (c(5, 3, 4, 3) + 0.1))
plot(f,
# increase line width
lwd = 1.5,
# set habplotype identifiers as labels
hap.names = hap.names(hh),
# find a place for the legend ...
legend.xy.coords = c(60000, 0.2)
)
# reset old margins
par(oldpar)
## ----newick1, eval = requireNamespace("ape", quietly = TRUE), fig.align = 'center', fig.cap = "Graphical output of the plot.phylo() function of package ape", fig.pos = '!h', fig.lp = 'fig:'----
newick <- as.newick(f,
allele = 0,
side = "left",
hap.names = hap.names(hh))
newick
library(ape)
tree <- ape::read.tree(text = newick)
plot(tree,
direction = "leftwards",
edge.color = "blue",
underscore = TRUE,
no.margin = TRUE)
## ----haplen11, fig.align = 'center', fig.cap = "Graphical output of the plot.haplen() function", fig.pos = '!h', fig.lp = 'fig:'----
h <- calc_haplen(f)
plot(h,
hap.names = hap.names(hh),
legend.xy.coords = c(70000,1.15))
## ----furcation12, fig.align = 'center', fig.cap = "Graphical output of the plot.haplen() function", fig.pos = '!h', fig.lp = 'fig:'----
f <- calc_furcation(hh, mrk = "rs6", phased = FALSE)
# set equal plot margins on left and right side and save old ones
oldpar <- par(mar = (c(5, 3, 4, 3) + 0.1))
plot(f,
# increase line width
lwd = 1.5,
# set haplotype identifiers as labels
hap.names = hap.names(hh),
# no place for a legend inside the plot
legend.xy.coords = "none")
# reset old margins
par(oldpar)
## ----haplen13, fig.align = 'center', fig.cap = "Graphical output of the plot.haplen() function", fig.pos = '!h', fig.lp = 'fig:'----
h <- calc_haplen(f)
plot(h, hap.names = hap.names(hh))
## -----------------------------------------------------------------------------
cat(readLines("example2.hap"),sep = "\n")
## -----------------------------------------------------------------------------
cat(readLines("example2.map"),sep = "\n")
## -----------------------------------------------------------------------------
cat(readLines("example2.vcf"), sep = "\n")
## -----------------------------------------------------------------------------
hh <- data2haplohh(hap_file = "example2.hap",
map_file = "example2.map",
allele_coding = "01")
## -----------------------------------------------------------------------------
hh <- data2haplohh(hap_file = "example2.hap",
map_file = "example2.map",
allele_coding = "01",
min_perc_geno.mrk = 50)
## -----------------------------------------------------------------------------
hh_map <- data2haplohh(hap_file = "example2.hap",
map_file = "example2.map",
allele_coding = "map",
min_perc_geno.mrk = 50,
verbose = FALSE)
identical(hh, hh_map)
hh_none <- data2haplohh(hap_file = "example2.hap",
map_file = "example2.map",
allele_coding = "none",
min_perc_geno.mrk = 50,
verbose = FALSE)
identical(hh, hh_none)
## ---- eval = requireNamespace("data.table", quietly = TRUE)-------------------
hh_vcf <- data2haplohh(hap_file = "example2.vcf",
min_perc_geno.mrk = 50,
vcf_reader = "data.table",
verbose = FALSE)
identical(hh, hh_vcf)
## ----hhplot2, fig.cap = "Graphical output of the plot.furcation() function"----
plot(hh)
## -----------------------------------------------------------------------------
res <- calc_ehh(hh,
mrk = "rs6",
include_nhaplo = TRUE,
include_zero_values = TRUE,
discard_integration_at_border = FALSE )
res
## ----ehh21, fig.align = 'center', fig.cap = "Graphical output of the plot.ehh() function", fig.pos = '!h', fig.lp = 'fig:'----
plot(res)
## -----------------------------------------------------------------------------
res <- calc_ehhs(hh,
mrk = "rs6",
include_nhaplo = TRUE,
include_zero_values = TRUE,
discard_integration_at_border = FALSE)
res
## ----ehhs21, fig.align = 'center', fig.cap = "Graphical output of the plot.ehh() function", fig.pos = '!h', fig.lp = 'fig:'----
plot(res)
## -----------------------------------------------------------------------------
scan <- scan_hh(hh, discard_integration_at_border = FALSE)
scan
## -----------------------------------------------------------------------------
scan_unpol <- scan_hh(hh,
discard_integration_at_border = FALSE,
polarized = FALSE)
scan_unpol
## -----------------------------------------------------------------------------
ihs <- ihh2ihs(scan, freqbin = 1)
ihs
## ----manhattan21, fig.align = 'center', fig.cap = "Graphical output of the manhattanplot() function", fig.pos = '!h', fig.lp = 'fig:'----
manhattanplot(ihs, threshold = c(-1.5, 1.5), ylim = c(-2.5,2.5), pch = 20)
## -----------------------------------------------------------------------------
hh_subset = subset(hh,
# exclude haplotypes with allele 2 at "rs6"
select.hap = haplo(hh)[ ,"rs6"] != 2,
min_perc_geno.mrk = 50)
scan <- scan_hh(hh_subset, discard_integration_at_border = FALSE)
scan
## ----manhattan22, fig.cap = "Graphical output of the manhattanplot() function", fig.pos = '!h', fig.lp = 'fig:'----
ihs <- ihh2ihs(scan, freqbin = 1, verbose = FALSE)
manhattanplot(ihs, threshold = c(-1.5, 1.5), ylim = c(-2.5,2.5), pch = 20)
## ----furcation21, fig.cap = "Graphical output of the plot.furcation() function", fig.pos = '!h', fig.lp = 'fig:'----
f <- calc_furcation(hh, mrk = "rs6")
# set equal plot margins on left and right side and save old ones
oldpar <- par(mar = (c(5, 3, 4, 3) + 0.1))
plot(f,
lwd = 1.5,
hap.names = hap.names(hh),
# no place for a legend inside the plot
legend.xy.coords = "none")
par(oldpar)
## ----newick2, eval = requireNamespace("ape", quietly = TRUE), fig.align = 'center', fig.cap = "Graphical output of the plot.phylo() function of package ape", fig.pos = '!h', fig.lp = 'fig:'----
newick <- as.newick(f,
allele = 0,
side = "left",
hap.names = hap.names(hh))
tree <- ape::read.tree(text = newick)
plot(tree,
direction = "leftwards",
edge.color = "blue",
underscore = TRUE,
no.margin = TRUE)
## ----haplen21, fig.align = 'center', fig.cap = "Graphical output of the plot.haplen() function", fig.pos = '!h', fig.lp = 'fig:'----
h <- calc_haplen(f)
plot(h, hap.names = hap.names(hh), legend.xy.coords = "none")
## -----------------------------------------------------------------------------
remove.example.files()
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