Description Usage Arguments Details Value Author(s) References See Also Examples
Functions for visualizing association test results by means of a Manhattan plot and for visualizing genotypes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39  ## S4 method for signature 'AssocTestResultRanges,missing'
plot(x, y, cutoff=0.05,
which=c("p.value", "p.value.adj", "p.value.resampled",
"p.value.resampled.adj"), showEmpty=FALSE,
as.dots=FALSE, pch=19, col=c("darkgrey", "grey"), scol="red",
lcol="red", xlab=NULL, ylab=NULL, ylim=NULL, lwd=1, cex=1,
cexXaxs=1, cexYaxs=1, srt=0, adj=c(0.5, 1), ...)
## S4 method for signature 'AssocTestResultRanges,character'
plot(x, y, cutoff=0.05,
which=c("p.value", "p.value.adj", "p.value.resampled",
"p.value.resampled.adj"), showEmpty=FALSE,
as.dots=FALSE, pch=19, col=c("darkgrey", "grey"), scol="red",
lcol="red", xlab=NULL, ylab=NULL, ylim=NULL, lwd=1, cex=1,
cexXaxs=1, cexYaxs=1, srt=0, adj=c(0.5, 1), ...)
## S4 method for signature 'AssocTestResultRanges,GRanges'
plot(x, y, cutoff=0.05,
which=c("p.value", "p.value.adj", "p.value.resampled",
"p.value.resampled.adj"), showEmpty=FALSE,
as.dots=FALSE, pch=19, col="darkgrey", scol="red", lcol="red",
xlab=NULL, ylab=NULL, ylim=NULL, lwd=1, cex=1,
cexXaxs=1, cexYaxs=1, ...)
## S4 method for signature 'GenotypeMatrix,missing'
plot(x, y, col="black",
labRow=NULL, labCol=NULL, cexXaxs=(0.2 + 1 / log10(ncol(x))),
cexYaxs=(0.2 + 1 / log10(nrow(x))), srt=90, adj=c(1, 0.5))
## S4 method for signature 'GenotypeMatrix,factor'
plot(x, y, col=rainbow(length(levels(y))),
labRow=NULL, labCol=NULL, cexXaxs=(0.2 + 1 / log10(ncol(x))),
cexYaxs=(0.2 + 1 / log10(nrow(x))), srt=90, adj=c(1, 0.5))
## S4 method for signature 'GenotypeMatrix,numeric'
plot(x, y, col="black", ccol="red", lwd=2,
labRow=NULL, labCol=NULL, cexXaxs=(0.2 + 1 / log10(ncol(x))),
cexYaxs=(0.2 + 1 / log10(nrow(x))), srt=90, adj=c(1, 0.5))
## S4 method for signature 'GRanges,character'
plot(x, y, alongGenome=FALSE,
type=c("r", "s", "S", "l", "p", "b", "c", "h", "n"),
xlab=NULL, ylab=NULL, col="red", lwd=2,
cexXaxs=(0.2 + 1 / log10(length(x))), cexYaxs=1,
frame.plot=TRUE, srt=90, adj=c(1, 0.5), ...)

x 
an object of class

y 
a character string, 
cutoff 
significance threshold 
which 
a character string specifying which pvalues to plot;
if “p.value” (default), raw pvalues are plotted.
Other options are “p.value.adj” (adjusted pvalues),
“p.value.resampled” (resampled pvalues), and
“p.value.resampled.adj” (adjusted resampled pvalues).
If the requested column is not present in the input object 
showEmpty 
if 
as.dots 
if 
pch 
plotting character used to plot a single pvalue, ignored
if 
col 
plotting color(s); see details below 
scol 
color for plotting significant pvalues (i.e. the ones passing the significance threshold) 
lcol 
color for plotting the significance threshold line 
xlab 
x axis label; if 
ylab 
y axis label; if 
ylim 
y axis limits; if 
lwd 
line thickness; in Manhattan plots, this parameter corresponds to the thickness of the significance threshold line. When plotting genotype matrices along with continuous traits, this is the thickness of the line that corresponds to the trait. 
cex 
scaling factor for plotting pvalues; see

labRow,labCol 
row and column labels; set to 
cexXaxs,cexYaxs 
scaling factors for axes labels 
ccol 
color of the line that plots the continuous trait along with a genotype matrix 
srt 
rotation angle of text labels on horizontal axis
(see 
adj 
adjustment of text labels on horizontal axis
(see 
alongGenome 
plot along the genome or per region (default); see details below. 
type 
type of plot; see 
frame.plot 
whether or not to frame the plotting area (see

... 
all other arguments are passed to

If plot
is called for an
AssocTestResultRanges
object without specifying the second argument y
,
a socalled Manhattan plot is produced. The x axis corresponds to the
genome on which the AssocTestResultRanges
x
is based and the y axis shows absolute values of
logtransformed pvalues. The which
argument determines
which pvalue is plotted, i.e. raw pvalues, adjusted pvalues,
resampled pvalues, or adjusted resampled pvalues. The cutoff
argument allows for setting a significance threshold above which
pvalues are plotted in a different color (see above).
The optional y
argument can be used for two purposes: (1) if it is
a character vector containing chromosome names (sequence names), it
can be used for specifying a subset of one or more chromosomes to be
plotted. (2) if y
is a GRanges
object of length
1 (if longer, plot
stops with an error), only the genomic
region corresponding to y
is plotted.
The col
argument serves for specifying the color for plotting
insignificant pvalues (i.e. the ones
above the significance threshold); if the number of colors is
smaller than the number of chromosomes, the vector is recycled.
If col
is a single color, all insignificant pvalues are
plotted in the same color. If col
has two elements (like the
default value), the insignificant pvalues of different chromosomes
are plotted with alternating colors. It is also possible to produce
density plots of pvalues by using semitransparent colors (see,
e.g., rgb
or hsv
for information on how
to use the alpha
channel).
If plot
is called for a GenotypeMatrix
object x
and no y
argument, the matrix is visualized in
a heatmaplike fashion, where two major alleles are displayed in white,
two minor alleles are displayed in the color passed as col
argument, and the heterozygotous case (one minor, one major) is
displayed in the color passed as col
argument, but with 50%
transparency. The arguments cexYaxs
and cexXaxs
can be
used to change the scaling of the axis labels.
If plot
is called for a GenotypeMatrix
object x
and a factor y
, then the factor y
is
interpreted as a binary trait. In this case, the rows of the genotype
matrix x
are reordered such that rows/samples with the same
label are plotted next to each other. Each such group can be plotted in a
different color. For this purpose, a vector of colors can be passed
as col
argument.
If plot
is called for a GenotypeMatrix
object x
and a numeric vector y
, then the vector y
is
interpreted as a continuous trait. In this case, the rows of the genotype
matrix x
are reordered according to the trait vector y
and the genotype matrix is plotted as described above. The trait
y
is superimposed in the plot in color ccol
and with
line width lwd
. If the null model has been trained with
covariates, it also makes sense to plot the genotype against the
null model residuals, since these are exactly the values that the
genotypes were tested against.
If plot
is called for a GRanges
object x
and a character string y
, then plot
checks whether x
has a metadata column named y
.
If it exists, this column is plotted against the regions in
x
. If alongGenome
is FALSE
(which is the
default), the regions
in x
are arranged along the horizontal plot axis
with equal widths and in the same order as contained in x
.
If the regions in x
are named, then the names are used as
axis labels and the argument cexXaxs
can be used to scale the
font size of the names. If alongGenome
is TRUE
,
the metadata column is plotted against genomic positions. The knots
of the curves are then positioned at the positions given in the
GRanges
object x
. For types “s”,
“S”, “l”, “p”, “b”, “c”, and
“h”, knots are placed in the middle of the genomic regions
contained in x
if they are longer than one base. For type
“r”, regions are plotted as lines exactly stretching between
the start and end coordinates of each region in x
.
returns an invisible numeric vector of length 2 containing the y axis limits
Ulrich Bodenhofer bodenhofer@bioinf.jku.at
http://www.bioinf.jku.at/software/podkat
AssocTestResultRanges
,
GRanges
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45  ## load genome description
data(hgA)
## partition genome into overlapping windows
windows < partitionRegions(hgA)
## load genotype data from VCF file
vcfFile < system.file("examples/example1.vcf.gz", package="podkat")
Z < readGenotypeMatrix(vcfFile)
## plot some fraction of the genotype matrix
plot(Z[, 1:25])
## read phenotype data from CSV file (continuous trait + covariates)
phenoFile < system.file("examples/example1log.csv", package="podkat")
pheno <read.table(phenoFile, header=TRUE, sep=",")
## train null model with all covariates in data frame 'pheno'
nm.log < nullModel(y ~ ., pheno)
## perform association test
res < assocTest(Z, nm.log, windows)
res.adj < p.adjust(res)
## plot results
plot(res)
plot(res, cutoff=1.e5, as.dots=TRUE)
plot(res.adj, which="p.value.adj")
plot(res.adj, reduce(windows[3:5]), which="p.value.adj")
## filter regions
res.adj.f < filterResult(res.adj, filterBy="p.value.adj")
## plot genotype grouped by target
sel < which(overlapsAny(variantInfo(Z), reduce(res.adj.f)))
plot(Z[, sel], factor(pheno$y))
plot(Z[, sel], residuals(nm.log), srt=45)
## compute contributions
contrib < weights(res.adj.f, Z, nm.log)
contrib[[1]]
## plot contributions
plot(contrib[[1]], "weight.raw")
plot(contrib[[1]], "weight.contribution", type="b", alongGenome=TRUE)

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