Usage
"forestplot"(x, ...)
"forestplot"(x, estimate = c("logor", "logodds", "or", "odds", "p"), level = 0.95, ...)
"forestplot"(x, ...)
forestplot.internal(x, annotate = TRUE, addfit = TRUE, xlim = NULL, alim = NULL, ylim = NULL, at = NULL, steps = 5, level = 0.95, digits = 2, refline = NULL, xlab = NULL, slab = NULL, mlab = NULL, ilab = NULL, ilab.xpos = NULL, ilab.pos = NULL, order = NULL, transf = FALSE, atransf = FALSE, targs = NULL, rows = NULL, efac = 1, pch = 15, psize = 1, col = "darkgrey", border = "darkgrey", cex = NULL, cex.lab = NULL, cex.axis = NULL, refcol = "red", predcol = refcol, ...)
Arguments
x
An object of class uwmwRes or uwmwEstimate.
...
parameters passed down to the internal
functions. These can be any of the following.
estimate
An optional character string defining
which measure should be plotted. It can take the values
logor, or, logodds, odds or
p (for displaying the probability of differential
expression, not the p-value!). Defaults to logor. Note
that this argument is ignored when plotting an
uwmwEstimate object.
annotate
A logical value indicating whether the
plot needs to be annotated, i.e. whether the values for
the chosen measure and confidence interval should be
displayed on the right of the plot. Defaults to TRUE
addfit
A logical value indicating whether the
reference measure should be plotted. See Details.
xlim
The horizontal limits of the plot region. If
unspecified, the function tries to set the horizontal
plot limits to some sensible values. Should not be used
by the user.
alim
the actual x axis limits. If unspecified, an
educated guess is taken by the function.
ylim
The vertical limits of the plot. If
unspecified, the function does what it thinks is best.
Should not be used by the user.
at
Position of the x axis tick marks and
corresponding labels are placed. If unspecified, the
function tries to position them at sensible values.
steps
An integer indicating the number of tick
marks on the X axis. Ignored when at is specified.
Defaults to 5
level
Numerical value between 0 and 1 to specify
the width of the confidence interval. Defaults to 0.95
(95% confidence interval).
digits
integer specyfing the number of decimal
places for tick mark labels and annotations. Can also be
a vector of two integers. In that case, the first value
specifies the number of decimal places for the
annotations, the second for the x axis labels.
refline
numerical value indicating where a
reference line should be drawn. An NA value will prevent
the line from being drawn. See Details.
xlab
title for the x axis. If unspecified, the
function tries to figure out the fitting title.
slab
optional vector with names for the displayed
genes.
mlab
optional character string giving a label to
the intercept estimate. If unspecified, this is created
in the function if necessary.
ilab
optional vector or matrix with character
strings providing additional information that can be
plotted next to the genes.
ilab.xpos
Vector of numerical values specifying
the x axis positions of the character vectors given via
ilab. This has to be specified when ilab is specified.
ilab.pos
integer from 1 to 4 specifying the
alignment of the character vector(s) given via ilab (2 is
right aligned, 4 is left aligned). Default is to center
the labels.
order
optional character string, character vector
or numerical vector specifying how the genes should be
ordered.
transf
optional argument specifying the name of a
function that should be used to transform the observed
effect sizes, summary estimates, fitted values and
confidence interval bounds (e.g., transf=exp).
Defaults to FALSE, which means that no
transformation is used.
atransf
optional argument specifying the name of a
function that should be used to transform the x-axis
labels and annotations (e.g., transf=exp). Defaults to
FALSE, which means that no transformation is
used.
targs
optional arguments needed by the function
specified via transf or atransf.
rows
optional vector specifying the horizontal
position for the plotted results. If unspecified, the
layout happens automatically. See Details and Examples
for more information.
efac
numerical value specifying the vertical
expansion of the arrows, summary estimate symbols and Ci
limits. Normally the default of 1 should work just fine.
pch
plotting symbol used for the observed effect
sizes. By default, it's a filled square.
psize
optional vector with the point sizes for the
observed effects. If set to NULL, the point sizes
are drawn proportional to the value of the log of the
test statistic. Defaults to 1.
cex
optional numerical value for expansion of text
and symbols. See also par. cex.lab
Optional numerical value for expansion of
the axis title.
cex.axis
Optional numerical value for expansion of
the x axis labels.
col
character string specifying the color used for
the individual estimates.
border
character string specifying the color used
for the border of the individual estimates.
refcol
Character string specyfying the color of
the reference line. Defaults to red.
predcol
character string specifying the color of
the estimated reference value. Ignored if estimate is
logor or or.