forestplot-methods: Making a forest plot of the results of uWMW
In unifiedWMWqPCR: Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Description Usage Arguments Details Value Warning Note Author(s) Examples

This function creates a forest plot indicating the (log) odds ratios, the (log) odds or the probabilities for the results of the unified Wilcoxon-Mann-Whitney test.

## S4 method for signature 'ANY'
forestplot(x, ...)

## S4 method for signature 'uwmwRes'
forestplot(x, estimate = c("logor", "logodds", "or",
  "odds", "p"), level = 0.95, ...)

## S4 method for signature 'uwmwEstimate'
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, ...)

`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.
`level`	Numerical value between 0 and 1 to specify the width of the confidence interval. Defaults to 0.95 (95% confidence interval).
`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
`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.
`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.
`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.
`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`.

The function has methods for uwmwRes and uwmwEstimate objects. When called for an uwmwRes object, the requested estimate is first calculated using getEstimate and the result is passed on to the next method.

Note that in either case, it is not possible to use the function on a subset of either type of object. The subsetting functions for uwmwRes and uwmwEstimate objects return matrices, and hence necessary information on the reference value is lost. To plot a subset of your data, use the order argument as shown in the examples.

Adding a reference value to the plot only makes sense when plotting the log(odds), odds or probabilities. If log(OR) or OR are plotted, addfit is set to FALSE.

The default settings plot a reference line at a location depending on the plotted estimate. For log(OR), the line is plotted at refline = 0. For OR, the line is plotted at refline = 1.

NULL invisibly

Although the internal function is shown here (merely for illustration of the arguments and defaults), the user shouldn't be calling this one directly. The function is not exported.

Thanks to the work of W.Viechtbauer, forestplot provides many possibilities for tweaking and customizing the plots. Many of the arguments work the same as in the function forest.rma (metafor package). You can always check the help file of forest.rma for more illustrations on the different arguments.

This function is currently implemented using an internal function that expects an uwmwEstimate object. In a future version, the internal function will be rewritten to be more generic. This will enable the definition of methods for other classes without need to change the internal function itself.

This code is adapted by Joris Meys from the function forest.rma (metafor package). The original function is written by W. Viechtbauer.

data(NBmat)
NBtest <- uWMW(NBmat, groups=NBgroups)
sigid <- which(pval(NBtest) < 0.05)
forestplot(NBtest,"logodds",order=sigid)

nameid <- c("hsa-mir-30a-3p","hsa-mir-30a-5p")
forestplot(NBtest,"p",order=nameid,addfit=FALSE,
           refline=NA,main="Comparison 30a")

forestplot(NBtest,"p",order=nameid,addfit=FALSE,
           refline=0.5,main="Comparison 30a",
           alim=c(0,1),xlim=c(-1,2),at=c(0,0.5,1))