Parameters used to choose what to plot and how. These parameters are given to plot.SCGLR
and pairs.SCGLR
.
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. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## 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)
|
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