rankplot-methods: Rankplot graphs

In EcoGenetics: Management and Exploratory Analysis of Spatial Data in Landscape Genetics

Description

This function generates a plot for a numeric or factor variable. A data frame/matrix with XY coordinates is required. The X and Y axes in the plot correspond to the rank of the X and Y coordinates, respectively.

Usage

eco.rankplot(
  input,
  XY,
  xlabel = NULL,
  ylabel = NULL,
  title = NULL,
  legendlabel = NULL,
  background = c("grey", "white"),
  ...
)

## S4 method for signature 'eco.lsa,missing,missing'
eco.rankplot(
  input,
  XY,
  xlabel,
  ylabel,
  title,
  legendlabel,
  background = c("grey", "white"),
  significant = TRUE,
  rescaled = FALSE,
  ns = NULL,
  interactivePlot = TRUE
)

## S4 method for signature 'numeric,dataframeORmatrix,missing'
eco.rankplot(
  input,
  XY,
  xlabel,
  ylabel,
  title,
  legendlabel,
  background = c("grey", "white"),
  interactivePlot = TRUE
)

## S4 method for signature 'factor,dataframeORmatrix,missing'
eco.rankplot(
  input,
  XY,
  xlabel,
  ylabel,
  title,
  legendlabel,
  background = c("grey", "white"),
  interactivePlot = TRUE
)

Arguments

input	Numeric/factor variable.
XY	Data frame or matrix with X-Y coordinates.
xlabel	Optional label for x axis.
ylabel	Optional label for y axis.
title	Optional title label.
legendlabel	Optional legend label.
background	Background color ("grey" or "white")-
...	Additional elements to the generic.
significant	Should only the individuals with significant result be colored?. This argument can be used with eco.lsa results. Default TRUE
rescaled	rescale values to [-1, 1] range?
ns	Color for non significant individuals, when significant = TRUE. This argument can be used with eco.lsa results.
interactivePlot	Show an interactive plot via plotly? (default: TRUE)

Author(s)

Leandro Roser [e-mail]

Examples

## Not run: 
data(eco3)

# The data set eco3 has 50 points in two sites, 
# but points are not visible in a usual X-Y plot, 
# due to the small distance among them in relation to the large
# distance between sites

var <- eco3[["P"]][,1]
plot(eco3[["XY"]], col = var)
x <- sample(1:100, 30)
y <- sample(1:100, 30)

# in a rankplot graph, the inter-individual distances are
# reduced to a single scale
rankeco3 <- eco.rankplot(var, eco3[["XY"]])
rankeco3

# the rankplot method supports the use of ggplot2 syntax with ggplot2 graphs
require(ggplot2)
rankeco3 <- eco.rankplot(var, eco3[["XY"]], interactivePlot = FALSE)
rankeco3 <- rankeco3 + theme_bw() + theme(legend.position="none")
rankeco3

## End(Not run)

EcoGenetics documentation built on July 8, 2020, 5:46 p.m.