longiPlot {imageData}

Plots longitudinal data from a Lemna Tec Scananalyzer

Description

Produce profile or longitudinal plots of the data from a Lemna Tec Scananalyzer using ggplot. A line is drawn for the data for each Snapshot.ID.Tag and the plot can be facetted so that a grid of plots is produced.

Usage

longiPlot(data, x = "xDays+44.5", response = "Area", individuals="Snapshot.ID.Tag", 
          x.title = "Days", y.title = "Area (1000 pixels)", title = NULL, 
          facet.x = "Treatment.1", facet.y =   "Smarthouse", labeller = NULL, 
          colour = "black", colour.column=NULL, colour.values=NULL, 
          alpha = 0.1, ggplotFuncs = NULL, printPlot = TRUE)

Arguments

data

A data.frame containing the data to be plotted.

x

A character giving the variable to be plotted on the x-axis.

response

A character specifying the response variable that is to be plotted on the y-axis.

individuals

A character giving the name(s) of the factor(s) that define the subsets of the data for which each subset corresponds to the response values for an individual.

x.title

Title for the x-axis.

y.title

Title for the y-axis.

title

Title for the plot.

facet.x

A data.frame giving the variable to be used to form subsets to be plotted in separate columns of plots. Use "." if a split into columns is not wanted.

facet.y

A data.frame giving the variable to be used to form subsets to be plotted in separate rows of plots. Use "." if a split into columns is not wanted.

labeller

A ggplot function for labelling the facets of a plot produced using the ggplot function. For more information see ggplot.

colour

A character specifying a single colour to use in drawing the lines for the profiles. If colouring according to the values of a variable is required then use colour.column.

colour.column

A character giving the name of a column in data over whose values the colours of the lines are to be varied. The colours can be specified using colour.values .

colour.values

A character vector specifying the values of the colours to use in drawing the lines for the profiles. If this is a named vector, then the values will be matched based on the names. If unnamed, values will be matched in order (usually alphabetical) with the limits of the scale.

alpha

A numeric specifying the degrees of transparency to be used in plotting. It is a ratio in which the denominator specifies the number of points (or line) that must be overplotted to give a solid cover.

ggplotFuncs

A list, each element of which contains the results of evaluating a ggplot function. It is created by calling the list function with a ggplot function call for each element.

printPlot

A logical indicating whether or not to print the plot.

Value

An object of class "ggplot", which can be plotted using print.

Author(s)

Chris Brien

See Also

ggplot, labeller.

Examples

data(exampleData)
longiPlot(data = longi.dat, response = "Area.smooth")

plt <- longiPlot(data = longi.dat, response = "Area.smooth", x.title = "DAP",  
                 y.title = "Area.smooth", x="xDays+35.42857143", printPlot=FALSE)
plt <- plt + ggplot2::geom_vline(xintercept=29, linetype="longdash", size=1) +
             ggplot2::scale_x_continuous(breaks=seq(28, 42, by=2)) + 
             ggplot2::scale_y_continuous(limits=c(0,750))
print(plt)

longiPlot(data = longi.dat, response = "Area.smooth", x.title = "DAP",  
          y.title = "Area.smooth", x="xDays+35.42857143", 
          ggplotFuncs = list(ggplot2::geom_vline(xintercept=29, linetype="longdash", 
                                                 size=1), 
                             ggplot2::scale_x_continuous(breaks=seq(28, 42, by=2)), 
                             ggplot2::scale_y_continuous(limits=c(0,750))))