- data
a data frame
- cond1
variable name corresponding to the first condition.
- cond2
variable name corresponding to the second condition.
- x, y
x and y variables, where x is a grouping variable and y contains
values for each group. Considered only when cond1 and cond2
are missing.
- id
variable name corresponding to paired samples' id. Used to connect
paired points with lines.
- color
points and box plot colors. To color by conditions, use color =
"condition".
- fill
box plot fill color. To change fill color by conditions, use fill
= "condition".
- 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".
- width
box plot width.
- point.size, line.size
point and line size, respectively.
- line.color
line color.
- linetype
line type.
- 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.
- label
the name of the column containing point labels. Can be also a
character vector with length = nrow(data).
- font.label
a list which can contain the combination of the following
elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic",
"bold.italic") and the color (e.g.: "red") of labels. For example font.label
= list(size = 14, face = "bold", color ="red"). To specify only the size and
the style, use font.label = list(size = 14, face = "plain").
- label.select
can be of two formats:
- 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.
- 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 be passed to ggpar().