plotProximity {rfPermute} | R Documentation |
Plot Random Forest Proximity Scores
Description
Create a plot of Random Forest proximity scores using multi-dimensional scaling.
Usage
plotProximity(
x,
dim.x = 1,
dim.y = 2,
class.cols = NULL,
legend.type = c("legend", "label", "none"),
legend.loc = c("top", "bottom", "left", "right"),
point.size = 2,
circle.size = 8,
circle.border = 1,
group.type = c("ellipse", "hull", "contour", "none"),
group.alpha = 0.3,
ellipse.level = 0.95,
n.contour.grid = 100,
label.size = 4,
label.alpha = 0.7,
plot = TRUE
)
Arguments
x |
a |
dim.x , dim.y |
numeric values giving x and y dimensions to plot from multidimensional scaling of proximity scores. |
class.cols |
vector of colors to use for each class. |
legend.type |
type of legend to use to label classes. |
legend.loc |
character keyword specifying location of legend.
Can be |
point.size |
size of central points. Set to |
circle.size |
size of circles around points indicating classification. Set to NULL for no circles. |
circle.border |
width of circle border. |
group.type |
type of grouping to display. Ignored for regression models. |
group.alpha |
value giving alpha transparency level for group shading.
Setting to |
ellipse.level |
the confidence level at which to draw the ellipse. |
n.contour.grid |
number of grid points for contour lines. |
label.size |
size of label if |
label.alpha |
transparency of label background. |
plot |
logical determining whether or not to show plot. |
Details
Produces a scatter plot of proximity scores for dim.x
and
dim.y
dimensions from a multidimensional scale (MDS) conversion of
proximity scores from a randomForest
object. For classification
models, points are colored according to original (inner)
and predicted (outer) class.
Value
a list with:
prox.mds |
the MDS scores of the selected dimensions |
g |
|
Author(s)
Eric Archer eric.archer@noaa.gov
Examples
library(randomForest)
data(symb.metab)
rf <- randomForest(type ~ ., symb.metab, proximity = TRUE)
# With confidence ellipses
plotProximity(rf)
# With convex hulls
plotProximity(rf, group.type = "hull")
# With contours
plotProximity(rf, group.type = "contour")
# Remove the points and just show ellipses
plotProximity(rf, point.size = NULL, circle.size = NULL, group.alpha = 0.5)
# Labels instead of a legend
plotProximity(rf, legend.type = "label", point.size = NULL, circle.size = NULL, group.alpha = 0.5)