Momocs (version 1.0.0)

plot2: Plots Principal Component Analysis ala ggplot2

Description

Displays a PCA object with many useful layers in morphometrics, notably morphological space.

Usage

plot2(x, ...)
"plot2"(x, fac = NULL, xax = "PC1", yax = "PC2", points = TRUE, shapes = TRUE, shapes_pos = "full", ellipse = FALSE, ellipseax = FALSE, ellipse_type = "t", ellipse_level = 0.5, stars = FALSE, chull = FALSE, text, text_abbreviatemin = 1, text_size = 5, center = TRUE, legend_position = "bottom", title = substitute(x), return_df = FALSE, ...)

Arguments

x

a PCA object

...

more arguments to be passed to xxx.

fac

(optionnal)

xax

the name of the component to plot on the x-axis, eg "PC1"

yax

the name of the component to plot on the y-axis, eg "PC2"

points

logical whether to draw points

shapes

logical whether to draw shapes

shapes_pos

a position parameter xxx either "axes", "full", "range", "circle", "xy" or a custom data.frame of positions

ellipse

logical whether to draw confidence ellipses

ellipseax

logical whether to draw confidence ellipses axes

ellipse_type

character one of the available type in ggplot2::stat_ellipse

ellipse_level

numeric the confidence level for ellipses

stars

logical whether to draw segments between every point and their group centroid

chull

logical whether to draw convex hull

text

numeric : 1 is for labelling every shape, 2 for group centroids, 3 is for evry shape using group names

text_abbreviatemin

numeric if not missing, the min.length sensu abbreviate

text_size

numeric to adjust the size of labels

center

logical whether to center the plot

legend_position

character for theme(legend.position), either "none", "top", "bottom", "left", "right"

title

character a title for the plot

return_df

logical whether to return ggplot or the data_frames behind

Value

a ggplot object or a list of data.frames :

• df0
• df_shp
• df_ellipseax
• df_stars
• df_chull

Details

Detail the df_s. Detail the calculations.

Examples

data(bot)
bp <- PCA(efourier(bot, 8))
plot2(bp)
plot2(bp, "type")
plot2(bp, "type", ellipse=TRUE)
# data(bot)

# bot$fac$fake <- factor(rep(letters[1:4], 10))
# bot$fac$fake2 <- c(runif(20), runif(20, 5, 10))
# xx + stat_density2d(aes(fill = ..level..), geom="polygon", alpha=0.1)