Plot Paired Data — ggpaired • ggpubr

Plot paired data.

Usage

ggpaired(
  data,
  cond1,
  cond2,
  x = NULL,
  y = NULL,
  id = NULL,
  color = "black",
  fill = "white",
  palette = NULL,
  width = 0.5,
  point.size = 1.2,
  line.size = 0.5,
  line.color = "black",
  linetype = "solid",
  title = NULL,
  xlab = "Condition",
  ylab = "Value",
  facet.by = NULL,
  panel.labs = NULL,
  short.panel.labs = TRUE,
  label = NULL,
  font.label = list(size = 11, color = "black"),
  label.select = NULL,
  repel = FALSE,
  label.rectangle = FALSE,
  ggtheme = theme_pubr(),
  jitter = 0,
  ...
)

Arguments

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:

a character vector specifying some labels to show.
a list containing one or the combination of the following components:
- top.up and top.down: to display the labels of the top up/down points. For example, label.select = list(top.up = 10, top.down = 4).
- criteria: to filter, for example, by x and y variables values, use this: label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')").

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(). Set ggtheme = NULL to skip applying a ggpubr theme, so the plot keeps ggplot2 default theme or the theme set globally via theme_set(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....

jitter

numeric value (default 0, no jitter) giving the amount of horizontal jitter added to the paired points to reduce overlap. Points are nudged sideways within [-jitter, jitter]; each subject (id) gets a single offset so its two points move together and the connecting line stays intact. Only the horizontal positions change (the values are never moved). Typical values are small relative to the box width (e.g. jitter = 0.05 to 0.1). jitter = 0 leaves the plot unchanged.

...

other arguments to be passed to be passed to ggpar().

Examples


# Example 1
# ::::::::::::::::::::::::::::::::::::::::::
before <- c(200.1, 190.9, 192.7, 213, 241.4, 196.9, 172.2, 185.5, 205.2, 193.7)
after <- c(392.9, 393.2, 345.1, 393, 434, 427.9, 422, 383.9, 392.3, 352.2)

d <- data.frame(before = before, after = after)
ggpaired(d,
  cond1 = "before", cond2 = "after",
  fill = "condition", palette = "jco"
)


# Example 2
# ::::::::::::::::::::::::::::::::::::::::::
ggpaired(ToothGrowth,
  x = "supp", y = "len",
  color = "supp", line.color = "gray", line.size = 0.4,
  palette = "npg"
)