Hi Sergey
I've attached a script with a ylim argument added to plotMeans.
If you are using Rcmdr, you can load this script via the Rcmdr File menu item
File
Open Script File
so save this plotMeans.R script somewhere,
and load it and run it in Rcmdr, then
do your plot command
plotMeans(DV, IV1, IV2, error.bars="se", ylim = c(27, 99))
or whatever your desired ylim values are.
HTH
Steven McKinney, Ph.D.
Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre
email: smckinney +at+ bccrc +dot+ ca
tel: 604-675-8000 x7561
BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C.
V5Z 1L3
Canada
________________________________________
From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of
Sergios (Sergey) Charntikov [sergios...@gmail.com]
Sent: November 5, 2009 7:51 PM
To: r-help@r-project.org
Subject: [R] Adjusting Yaxis (ylim) limits on a plotMeans(DV, IV1, IV2,
error.bars="se")
Hello everyone,
I have tried to look for this everywhere and so far have no luck. I have a
plotMeans(DV, IV1, IV2, error.bars="se") graph that plots my data
(DV-continuous, IVs are factors, IV1 - two levels, IV2-four levels). I am
trying to increase a scale of my y-axis (to be consistent with my other
graphs), but unfortunately nothing works with "plotMeans" function, which is
the only one I see so fat to plot what I need. Could anyone provide any
suggestions or advice?
Thank you.
Sergey (UNL, Behavioral Psychopharmacology Lab)
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
plotMeans <-
function (response, factor1, factor2, error.bars = c("se", "sd",
"conf.int", "none"), level = 0.95, xlab = deparse(substitute(factor1)),
ylab = paste("mean of", deparse(substitute(response))), legend.lab =
deparse(substitute(factor2)),
main = "Plot of Means", pch = 1:n.levs.2, lty = 1:n.levs.2,
col = palette(), ylim = NULL)
{
if (!is.numeric(response))
stop(gettextRcmdr("Argument response must be numeric."))
xlab
ylab
legend.lab
error.bars <- match.arg(error.bars)
if (missing(factor2)) {
if (!is.factor(factor1))
stop(gettextRcmdr("Argument factor1 must be a factor."))
valid <- complete.cases(factor1, response)
factor1 <- factor1[valid]
response <- response[valid]
means <- tapply(response, factor1, mean)
sds <- tapply(response, factor1, sd)
ns <- tapply(response, factor1, length)
if (error.bars == "se")
sds <- sds/sqrt(ns)
if (error.bars == "conf.int")
sds <- qt((1 - level)/2, df = ns - 1, lower.tail = FALSE) *
sds/sqrt(ns)
sds[is.na(sds)] <- 0
yrange <- if (error.bars != "none")
c(min(means - sds, na.rm = TRUE), max(means + sds,
na.rm = TRUE))
else range(means, na.rm = TRUE)
levs <- levels(factor1)
n.levs <- length(levs)
if ( is.null(ylim) ) {
plot(c(1, n.levs), yrange, type = "n", xlab = xlab, ylab = ylab,
axes = FALSE, main = main)
} else {
plot(c(1, n.levs), yrange, type = "n", xlab = xlab, ylab = ylab,
axes = FALSE, main = main, ylim = ylim)
}
points(1:n.levs, means, type = "b", pch = 16, cex = 2)
box()
axis(2)
axis(1, at = 1:n.levs, labels = levs)
if (error.bars != "none")
arrows(1:n.levs, means - sds, 1:n.levs, means + sds,
angle = 90, lty = 2, code = 3, length = 0.125)
}
else {
if (!(is.factor(factor1) | is.factor(factor2)))
stop(gettextRcmdr("Arguments factor1 and factor2 must be factors."))
valid <- complete.cases(factor1, factor2, response)
factor1 <- factor1[valid]
factor2 <- factor2[valid]
response <- response[valid]
means <- tapply(response, list(factor1, factor2), mean)
sds <- tapply(response, list(factor1, factor2), sd)
ns <- tapply(response, list(factor1, factor2), length)
if (error.bars == "se")
sds <- sds/sqrt(ns)
if (error.bars == "conf.int")
sds <- qt((1 - level)/2, df = ns - 1, lower.tail = FALSE) *
sds/sqrt(ns)
sds[is.na(sds)] <- 0
yrange <- if (error.bars != "none")
c(min(means - sds, na.rm = TRUE), max(means + sds,
na.rm = TRUE))
else range(means, na.rm = TRUE)
levs.1 <- levels(factor1)
levs.2 <- levels(factor2)
n.levs.1 <- length(levs.1)
n.levs.2 <- length(levs.2)
if (length(pch) == 1)
pch <- rep(pch, n.levs.2)
if (length(col) == 1)
col <- rep(col, n.levs.2)
if (length(lty) == 1)
lty <- rep(lty, n.levs.2)
if (n.levs.2 > length(col))
stop(sprintf(gettextRcmdr("Number of groups for factor2, %d,
exceeds number of distinct colours, %d."),
n.levs.2, length(col)))
if ( is.null(ylim) ) {
plot(c(1, n.levs.1 * 1.4), yrange, type = "n", xlab = xlab,
ylab = ylab, axes = FALSE, main = main)
} else {
plot(c(1, n.levs.1 * 1.4), yrange, type = "n", xlab = xlab,
ylab = ylab, axes = FALSE, main = main, ylim = ylim)
}
box()
axis(2)
axis(1, at = 1:n.levs.1, labels = levs.1)
for (i in 1:n.levs.2) {
points(1:n.levs.1, means[, i], type = "b", pch = pch[i],
cex = 2, col = col[i], lty = lty[i])
if (error.bars != "none")
arrows(1:n.levs.1, means[, i] - sds[, i], 1:n.levs.1,
means[, i] + sds[, i], angle = 90, code = 3,
col = col[i], lty = lty[i], length = 0.125)
}
x.posn <- n.levs.1 * 1.1
y.posn <- sum(c(0.1, 0.9) * par("usr")[c(3, 4)])
text(x.posn, y.posn, legend.lab, adj = c(0, -0.5))
legend(x.posn, y.posn, levs.2, pch = pch, col = col,
lty = lty)
}
invisible(NULL)
}
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
