- data
a data frame
- x, y
x and y variables for drawing.
- combine
logical value. Default is FALSE. Used only when y is a vector
containing multiple variables to plot. If TRUE, create a multi-panel plot by
combining the plot of y variables.
- merge
logical or character value. Default is FALSE. Used only when y is
a vector containing multiple variables to plot. If TRUE, merge multiple y
variables in the same plotting area. Allowed values include also "asis"
(TRUE) and "flip". If merge = "flip", then y variables are used as x tick
labels and the x variable is used as grouping variable.
- color, fill
point colors.
- palette
the color palette to be used for coloring or filling by groups.
Allowed values include "grey" for grey color palettes; brewer palettes e.g.
"RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and
scientific journal palettes from ggsci R package, e.g.: "npg", "aaas",
"lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
- shape
point shape. See show_point_shapes.
- size
Numeric value (e.g.: size = 1). change the size of points and
outlines.
- point
logical value. If TRUE, show points.
- rug
logical value. If TRUE, add marginal rug.
- title
plot main title.
- xlab
character vector specifying x axis labels. Use xlab = FALSE to
hide xlab.
- ylab
character vector specifying y axis labels. Use ylab = FALSE to
hide ylab.
- facet.by
character vector, of length 1 or 2, specifying grouping
variables for faceting the plot into multiple panels. Should be in the data.
- panel.labs
a list of one or two character vectors to modify facet panel
labels. For example, panel.labs = list(sex = c("Male", "Female")) specifies
the labels for the "sex" variable. For two grouping variables, you can use
for example panel.labs = list(sex = c("Male", "Female"), rx = c("Obs",
"Lev", "Lev2") ).
- short.panel.labs
logical value. Default is TRUE. If TRUE, create short
labels for panels by omitting variable names; in other words panels will be
labelled only by variable grouping levels.
- add
allowed values are one of "none", "reg.line" (for adding linear
regression line) or "loess" (for adding local regression fitting).
- add.params
parameters (color, size, linetype) for the argument 'add';
e.g.: add.params = list(color = "red").
- conf.int
logical value. If TRUE, adds confidence interval.
- conf.int.level
Level controlling confidence region. Default is 95%.
Used only when add != "none" and conf.int = TRUE.
- fullrange
should the fit span the full range of the plot, or just the
data. Used only when add != "none".
- ellipse
logical value. If TRUE, draws ellipses around points.
- ellipse.level
the size of the concentration ellipse in normal
probability.
- ellipse.type
Character specifying frame type. Possible values are
"convex", "confidence" or types supported by
stat_ellipse() including one of c("t", "norm",
"euclid") for plotting concentration ellipses.
"convex": plot convex hull of a set o points.
"confidence": plot confidence ellipses arround group mean points as
FactoMineR::coord.ellipse().
"t":
assumes a multivariate t-distribution.
"norm": assumes a
multivariate normal distribution.
"euclid": draws a circle with
the radius equal to level, representing the euclidean distance from the
center. This ellipse probably won't appear circular unless
coord_fixed() is applied.
- ellipse.alpha
Alpha for ellipse specifying the transparency level of
fill color. Use alpha = 0 for no fill color.
- ellipse.border.remove
logical value. If TRUE, remove ellipse border lines.
- mean.point
logical value. If TRUE, group mean points are added to the
plot.
- mean.point.size
numeric value specifying the size of mean points.
- star.plot
logical value. If TRUE, a star plot is generated.
- star.plot.lty, star.plot.lwd
line type and line width (size) for star
plot, respectively.
- label
the name of the column containing point labels. Can be also a
character vector with length = nrow(data).
- font.label
a vector of length 3 indicating respectively the size
(e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and
the color (e.g.: "red") of point labels. For example font.label =
c(14, "bold", "red"). To specify only the size and the style, use
font.label = c(14, "plain").
- font.family
character vector specifying font family.
- label.select
character vector specifying some labels to show.
- repel
a logical value, whether to use ggrepel to avoid overplotting
text labels or not.
- label.rectangle
logical value. If TRUE, add rectangle underneath the
text, making it easier to read.
- parse
If TRUE, the labels will be parsed into expressions and
displayed as described in ?plotmath.
- cor.coef
logical value. If TRUE, correlation coefficient with the
p-value will be added to the plot.
- cor.coeff.args
a list of arguments to pass to the function
stat_cor for customizing the displayed correlation
coefficients. For example: cor.coeff.args = list(method = "pearson",
label.x.npc = "right", label.y.npc = "top").
- cor.method
method for computing correlation coefficient. Allowed
values are one of "pearson", "kendall", or "spearman".
- cor.coef.coord
numeric vector, of length 2, specifying the x and y
coordinates of the correlation coefficient. Default values are NULL.
- cor.coef.size
correlation coefficient text font size.
- ggp
a ggplot. If not NULL, points are added to an existing plot.
- show.legend.text
logical. Should text be included in the legends? NA,
the default, includes if any aesthetics are mapped. FALSE never includes,
and TRUE always includes.
- ggtheme
function, ggplot2 theme name. Default value is theme_pubr().
Allowed values include ggplot2 official themes: theme_gray(), theme_bw(),
theme_minimal(), theme_classic(), theme_void(), ....
- ...
other arguments to be passed to geom_point
and ggpar.