lineplot.CI {sciplot}

Line Plot with CI

Description

Lineplot of the mean and standard error (or other summary statistics) of a response variable for one-way or higher experimental designs.

Usage

lineplot.CI(x.factor, response, group=NULL, type="b", xlab=NULL, ylab=NULL,
    x.cont=FALSE, legend=TRUE, leg.lab=NULL, fixed=FALSE,
    x.leg=NULL, y.leg=NULL, cex.leg=1, ncol=1,
    pch=c(16, 21, 15, 22, 17, 24, c(3:14)), 
    fun = function(x) mean(x, na.rm=TRUE),
    ci.fun= function(x) c(fun(x)-se(x), fun(x)+se(x)),
    err.width = if(length(levels(as.factor(x.factor))) > 10) 0 else 0.1,
    err.col = col, err.lty = 1, 
    xlim=NULL, ylim=NULL, cex=NULL, lwd=NULL, col="black", cex.axis=1,
    xaxt="s", data=NULL, subset=NULL, ...)

Arguments

x.factor

a factor (required) whose levels will form the x axis.

response

a numeric variable giving the response.

group

grouping factor (optional) whose levels will form the traces.

type

the type of plot: lines, points, or both. Defaults to both.

xlab

default x-axis label. If not specified will parse name from x.factor. To leave blank set to NA

ylab

default y-axis label. If not specified will parse name from response. To leave blank set to NA

x.cont

logical. Treat x.factor as a continuous variable?

legend

logical. Should a legend be included?

leg.lab

legend labels for trace factors.

fixed

logical. Should the legend be in the order of the levels of 'trace.factor' or in the order of the traces at their right-hand ends?

x.leg, y.leg

optional values to over ride the default legend placement.

cex.leg

character expansion value for legend labels.

ncol

number of columns to use for legend.

pch

a vector of plotting symbols or characters.

fun

the function to compute the summary statistic. Should return a single real value. Defaults to mean with NA values removed.

ci.fun

the functions to compute the CI. Should return a vector of length 2 defining the lower and upper limits of the CI's. Defaults to the mean +/- 1 standard error, with NA values removed.

err.width

set width of whiskers for error bars.

err.col

color for error bars. Defaults to col.

err.lty

line type for error bars.

xlim, ylim

range for x and y axes.

cex

overall plot character expansion value.

lwd

deterimines line width.

col

default color(s) for plot.

cex.axis

character expansion value for axis labels.

xaxt

should x-axis be drawn?

data

an optional data frame.

subset

an optional expression indicating the subset of the rows of 'data' that should be used in the plot.

...

further graphical parameters.

Details

Plots a response as a function of treatment (factor) combinations for one-way and higher designs. This is a "wrapper" function for plot in one-way designs and interaction.plot in higher-way designs that adds confidence intervals - those functions should be consulted for details. Notable changes from the defaults for interaction.plot include the removal of NA values by default, options to specify a subset of data and greater flexibility in the placement of legends. This function replicates some of the functionality of plotmeans from the package gplots, with differences in the treatment of two-way and higher designs.

See Also

interaction.plot, se

Examples

data(ToothGrowth)

# One way design
lineplot.CI(x.factor = dose, response = len, data = ToothGrowth) 

# Two-way design with options
lineplot.CI(dose, len, group = supp, data = ToothGrowth, cex = 2,
            xlab = "Dose", ylab = "Growth", cex.lab = 1.5, x.leg = 1,
            col = c("blue","red"), pch = c(16,16))