Multiple comparisons plot that gives independent user control over the appearance of the significant and not significant comparisons.

Multiple comparisons plot that gives independent user control over the appearance of the significant and not significant comparisons. In R, both plot.multicomp plot.multicomp.hh coerce their argument to an "glht" object and plots that with the appropriate plot method. In R, plot.multicomp.adjusted replaces the bounds calculated by multcomp:::confint.glht with bounds based on a common standard error for a set of anova tables that are partitioned for the simple effects on an analysis conditioned on the levels of one of the factors. In S-Plus, plot.multicomp.hh augments the standard plot.multicomp to give additional user arguments to control the appearance of the plot.

plotMatchMMC uses the plot.multicomp.hh code. plotMatchMMC must immediately follow a plot of an mmc.multicomp object and is applied to either the $mca or $lmat component of the mmc.multicomp object. plotMatchMMC is used as a tiebreaker plot for the MMC plot. plotMatchMMC matches the horizontal scaling of the MMC plot and displays the individual contrasts in the same order as the MMC plot. See mmc for examples.

These functions are no longer recommended. Use mmcplot instead.

## S3 method for class 'multicomp':
plot(x, ...) ## R only

## S3 method for class 'multicomp.hh': plot(x, ylabel = x$ylabel, href = 0, uniform = TRUE, = c(0.2, 0.9, 0.1, 0.9), x.label.adj=1, xrange.include=href, xlim,, col.signif=1, col.not.signif=1, lty.signif=4, lty.not.signif=4, lwd.signif=1, lwd.not.signif=1, ..., xlabel.print=TRUE, y.axis.side=2, ylabel.inside=FALSE)

plotMatchMMC(x, ..., xlabel.print=FALSE, cex.axis=par()$cex.axis, col.signif='red', main="", ylabel.inside=FALSE, y.axis.side=4, adjusted=FALSE)

A "multicomp" object. plotMatchMMC will also accept a mmc.multicomp object. It will use the lmat component if there is one, otherwise it will use the mca component.
Y label on graph.
Y labels are on the left by default when plotting a "multicomp" object. We move them to the right when matching the x-axis of an MMC plot.
other arguments to plot.multicomp.
Logical value, if FALSE (the default), the plotMatchMMC right-axis labels are in the margin. If TRUE, the right-axis labels are in the figure area. Setting the argument to TRUE makes sen
reference line for the intervals. The default is 0. S-Plus only.
xlim will be extended to include these values. S-Plus only.
S-Plus only. Logical value, if TRUE and the plots fill more than one page, the scale will be uniform across pages.
S-Plus only. Value for par("plt") to make better use of the space on the plotting page.
S-Plus only. This is the par("adj") applied to the x-location of the y.labels on the multicomp plot.
x-range of the plot.
The default S-Plus plot.multicomp hardwires this to 21, which allows for all pairwise comparisons of 7 levels taken 2 at a time. The HH plot.multicomp makes it a variable. Use it together with
lty.signif, lwd.signif
Line type, and line width for significant comparisons. S-Plus only.
Color for significant comparisons. S-Plus only for plot.multicomp. Both R and S-Plus for plotMatchMMC.
col.not.signif, lty.not.signif, lwd.not.signif
Color, line type, and line width for non-significant comparisons. S-Plus only.
logical. When TRUE, the caption under the plot is printed. When FALSE, the caption under the plot is not printed. It is helpful to set this to FALSE when the multicomp plot is used as
cex for axis ticklabels.
Main title for plot.
Logical. When TRUE, HH:::plot.multicomp.adjusted is used to replace the standard confidence bounds calculated by multcomp:::confint.glht, with bounds calculated by as.multicomp.glht w

  • plot.multicomp plots a "multicomp" object. In S-Plus, this masks the standard plot.multicomp in order to provide additional arguments for controlling the appearance. It defaults to the standard appearance. In R, it coerces its argument to a "glht" object and plots that with the appropriate plot method.


The multiple comparisons calculations in R and S-Plus use completely different packages.#ifndef S-Plus Multiple comparisons in R are based on glht. Multiple comparisons in S-Plus are based on multicomp. #endif #ifdef S-Plus Multiple comparisons in R are based on glht. Multiple comparisons in S-Plus are based on multicomp. #endif The MMC plot in the HH package is the same in both systems. The details of getting the plot differ.


Heiberger, Richard M. and Holland, Burt (2004b). Statistical Analysis and Data Display: An Intermediate Course with Examples in S-Plus, R, and SAS. Springer Texts in Statistics. Springer. ISBN 0-387-40270-5.

Heiberger, R. M. and Holland, B. (2006). "Mean--mean multiple comparison displays for families of linear contrasts." Journal of Computational and Graphical Statistics, 15:937--955.

See Also

mmc in both languages,#ifndef S-Plus glht. #endif #ifdef S-Plus multicomp. #endif

  • plot.multicomp
  • plot.multicomp.hh
  • plot.multicomp.adjusted
  • plotMatchMMC
## data and ANOVA

catalystm1.aov <- aov(concent ~ catalyst, data=catalystm)

catalystm.mca <-
if.R(r=glht(catalystm1.aov, linfct = mcp(catalyst = "Tukey")),
     s=multicomp(catalystm1.aov, plot=FALSE))
     r=plot(confint(catalystm.mca, calpha=qtukey(.95, 4, 12)/sqrt(2))))
       ## calpha is strongly recommended in R with a large number of levels
       ## See ?MMC for details.
Documentation reproduced from package HH, version 3.1-25, License: GPL (>= 2)

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