PlotVariations {Evomorph}

Plot shapes

Description

Plot the differences between a set of morphometric shapes and a reference

Usage

PlotVariations(shapes, reference, path, save = F, w = 6, h = 6, d = 100, c_ref = "red", 
 c_target = "black", s_ref = 3, s_target = 2)

Arguments

shapes

Landmark data of shapes (list of matrices)

reference

Landmark data of reference shape (matrix type)

path

Path where results will be saved (Default: working directory)

c_ref

Color of the points representing the reference shape (Default c_ref="red")

c_target

Color of the points representing the target shape (Default c_target="black")

s_ref

Size of the points representing the reference shape (Default s_ref=3)

s_target

Size of the points representing the target shape (Default s_target=2)

save

A logical value. If TRUE, the function will save the plot as jpeg images in the indicated in path

This parameters are used to modify stored graph (save = TRUE):

w

Units of width of the graph in inches (Default w = 6)

h

Units of height of the graph in inches(Default h = 6)

d

Number of dpi (resolution) of the graph. (Default d = 6)

Details

The function uses package ggplot2 (Wickman 2009) to create multiple plots representing the variations between a list of target shapes and a reference (consensus shape or another specimen data). If save=TRUE it creates a folder (named day_hh_mm) and stores the plots as images (.jpeg) at the provided path (if not provided it will store them in the working directory). There are several parameters for modify the graph for a suitable representation. This function could be used for example to analyze morphological variations of species over generations.

Author(s)

Cabrera Juan Manuel

References

H. Wickham. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York, 2009.

See Also

SimEvo

Examples

 
data("aegla_consensus")
data("simulated_shapes")

#Sample one individual from simulated_shapes dataset

simu<-simulated_shapes[100]

#Create a shape variation graphic

graph<-PlotVariations(simu,aegla_consensus)

#Red dots represent the landmark coordinates of the reference shape and black
# dots represent the target shape. The length of the segments represent 
# distances between pairs of homologous landmarks
  
graph[[1]]