Scatter plot matrix

Produces a scatter plot matrix between the selected columns of the outcomes matrix \(Y\) choosing specific colors and symbols for up to four factors from the design on the upper and lower diagonals.

Usage

plotScatterM(
  Y = NULL,
  design = NULL,
  lmpDataList = NULL,
  cols,
  labelVector = NULL,
  title = "Scatterplot matrix",
  varname.colorup = NULL,
  varname.colordown = NULL,
  varname.pchup = NULL,
  varname.pchdown = NULL,
  vec.colorup = NULL,
  vec.colordown = NULL,
  vec.pchup = NULL,
  vec.pchdown = NULL
)

Arguments

Y

\(n \times m\) matrix with \(n\) observations and \(m\) variables. Can be NULL if lmpDataList is defined.

design

A \(n \times k\) "freely encoded" experimental design data.frame. Can be NULL if lmpDataList is defined.

lmpDataList

If not NULL, a list with outcomes, design and formula, as outputted by data2LmpDataList.

cols

A vector with either the column names of the \(Y\) matrix to plot (character) or the column index positions.

labelVector

Labels to display on the diagonal. If NULL, the column names are deduced from cols.

title

Title of the graph.

varname.colorup

A character string with the name of the variable used to color the upper triangle.

varname.colordown

A character string with the name of the variable used to color the lower triangle.

varname.pchup

A character string with the name of the variable used to mark points for the upper triangle.

varname.pchdown

A character string with the name of the variable used to mark points for the lower triangle.

vec.colorup

A color vector (character or numeric) with a length equal to the number of levels of varname.colorup.

vec.colordown

A color vector (character or numeric) with a length equal to the number of levels of varname.colordown.

vec.pchup

A symbol vector (character or numeric) with a length equal to the number of levels of varname.pchup.

vec.pchdown

A symbol vector (character or numeric) with a length equal to the number of levels of varname.pchdown.

Value

A matrix of scatter plots.

Details

Either Y or lmpDataList need to be defined. If both are given, the priority goes to Y. The same rule applies for design or lmpDataList.

Examples

data("UCH")

# basic usage
plotScatterM(
  Y = UCH$outcomes, design = UCH$design, cols = c(1:4)
)

# equivalent to:
plotScatterM(
  lmpDataList = UCH, cols = c(1:4)
)


# with optionnal arguments
plotScatterM(
  Y = UCH$outcomes, design = UCH$design, cols = c(1:4),
  varname.colorup = "Hippurate", varname.colordown = "Citrate",
  varname.pchup = "Time", varname.pchdown = "Day",
  vec.colorup = c(2, 4, 1),
  vec.colordown = c("orange", "purple", "green"),
  vec.pchup = c(1, 2), vec.pchdown = c("a", "b")
)