customize: Plot customization

Description Details Examples

Description

Parameters used to choose what to plot and how. These parameters are given to plot.SCGLR and pairs.SCGLR.

Details

Parameter name can be abbreviated (e.g. pred.col will be understood as predictors.color).
Options can be set globally using options("plot.SCGLR"). It will then provide default values that can be further overriden by giving explicit parameter value.

parameter name type (default value). Description.
title string (NULL). Main title of plot (override built-in).
labels.auto logical (TRUE). Should covariate or predictor labels be aligned with arrows.
labels.offset numeric (0.01). Offset by which labels should be moved from tip of arrows.
labels.size numeric (1). Relative size for labels. Use it to globally alter label size.
expand numeric (1). Expand factor for windows size. Use it for example to make room for clipped labels.
threshold numeric. All covariates and/or predictors whose sum of square correlations with the two components of the plane lower than this threshold will be ignored.
observations logical (FALSE). Should we draw observations.
observations.size numeric (1). Point size.
observations.color character ("black"). Point color.
observations.alpha numeric (1). Point transparency.
observations.factor logical (FALSE). Paint observations according to factor (specify factor).
predictors logical or array of characters (FALSE). Should we draw predictors and optionally which one (TRUE means all).
predictors.color string ("red"). Base color used to draw predictors.
predictors.alpha numeric (1). Overall transparency for predictors (0 is transparent, 1 is opaque).
predictors.arrows logical (TRUE). Should we draw arrows for predictors.
predictors.arrows.color string (predictors.color). Specific color for predictor arrows.
predictors.arrows.alpha numeric (predictors.alpha). Transparency for predictor arrows.
predictors.labels logical (TRUE). Should we draw labels for predictors.
predictors.labels.color string (predictors.color). Specific color for predictor labels.
predictors.labels.alpha numeric (predictors.alpha). Transparency for predictor labels.
predictors.labels.size numeric (labels.size). Specific size for predictor labels.
predictors.labels.auto logical (labels.auto). Should predictor labels be aligned with arrows.
covariates logical or array of characters (TRUE). Should we draw covariates and optionally which one (TRUE means all).
covariates.color string ("black"). Base color used to draw covariates.
covariates.alpha numeric (1). Overall transparency for covariates (0 is transparent, 1 is opaque).
covariates.arrows logical (TRUE). Should we draw arrows for covariates.
covariates.arrows.color string (covariates.color). Specific color for covariate arrows.
covariates.arrows.alpha numeric (covariates.alpha). Transparency for covariate arrows.
covariates.labels logical (TRUE). Should we draw labels for predictors.
covariates.labels.color string (covariates.color). Specific color for predictor labels.
covariates.labels.alpha numeric (covariates.alpha). Transparency for covariate labels.
covariates.labels.size numeric (labels.size). Specific size for covariate labels.
covariates.labels.auto logical (labels.auto). Should covariate labels be aligned with arrows.
factor logical or character (FALSE). Should we draw a factor chosen among additionnal variables (TRUE mean first one).
factor.points logical (TRUE). Should symbol be drawn for factors.
factor.points.size numeric (4). Symbol size.
factor.points.shape numeric (13). Point shape.
factor.labels logical (TRUE). Should factor labels be drawn.
factor.labels.color string ("black"). Color used to draw labels.
factor.labels.size numeric (labels.size). Specific size for factor labels.

Examples

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## Not run: 
# setting parameters
plot(genus.scglr)
plot(genus.scglr, predictors=TRUE)
plot(genus.scglr, predictors=TRUE, pred.arrows=FALSE)

# setting global style
options(plot.SCGLR=list(predictors=TRUE, pred.arrows=FALSE))
plot(genus.scglr)

# setting custom style
myStyle <- list(predictors=TRUE, pred.arrows=FALSE)
plot(genus.scglr, style=myStyle)

## End(Not run)

SCGLR documentation built on May 1, 2019, 8 p.m.