ggdotplot: Dot plot

In ggpubr: 'ggplot2' Based Publication Ready Plots

Dot plot

Description

Create a dot plot.

Usage

ggdotplot(
  data,
  x,
  y,
  combine = FALSE,
  merge = FALSE,
  color = "black",
  fill = "lightgray",
  palette = NULL,
  title = NULL,
  xlab = NULL,
  ylab = NULL,
  facet.by = NULL,
  panel.labs = NULL,
  short.panel.labs = TRUE,
  size = NULL,
  binwidth = NULL,
  select = NULL,
  remove = NULL,
  order = NULL,
  add = "mean_se",
  add.params = list(),
  error.plot = "pointrange",
  label = NULL,
  font.label = list(size = 11, color = "black"),
  label.select = NULL,
  repel = FALSE,
  label.rectangle = FALSE,
  ggtheme = theme_pubr(),
  ...
)

Arguments

data	a data frame
x	character string containing the name of x variable.
y	character vector containing one or more variables to plot
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	outline color.
fill	fill color.
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".
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.
size	Numeric value (e.g.: size = 1). change the size of points and outlines.
binwidth	numeric value specifying bin width. use value between 0 and 1 when you have a strong dense dotplot. For example binwidth = 0.2.
select	character vector specifying which items to display.
remove	character vector specifying which items to remove from the plot.
order	character vector specifying the order of items.
add	character vector for adding another plot element (e.g.: dot plot or error bars). Allowed values are one or the combination of: "none", "dotplot", "jitter", "boxplot", "point", "mean", "mean_se", "mean_sd", "mean_ci", "mean_range", "median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see ?desc_statby for more details.
add.params	parameters (color, shape, size, fill, linetype) for the argument 'add'; e.g.: add.params = list(color = "red").
error.plot	plot type used to visualize error. Allowed values are one of c("pointrange", "linerange", "crossbar", "errorbar", "upper_errorbar", "lower_errorbar", "upper_pointrange", "lower_pointrange", "upper_linerange", "lower_linerange"). Default value is "pointrange" or "errorbar". Used only when add != "none" and add contains one "mean_*" or "med_*" where "*" = sd, se, ....
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 variabes 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(). Allowed values include ggplot2 official themes: theme_gray(), theme_bw(), theme_minimal(), theme_classic(), theme_void(), ....
...	other arguments to be passed to geom_dotplot, ggpar and facet.

Details

The plot can be easily customized using the function ggpar(). Read ?ggpar for changing:

• main title and axis labels: main, xlab, ylab

• axis limits: xlim, ylim (e.g.: ylim = c(0, 30))

• axis scales: xscale, yscale (e.g.: yscale = "log2")

• color palettes: palette = "Dark2" or palette = c("gray", "blue", "red")

• legend title, labels and position: legend = "right"

• plot orientation : orientation = c("vertical", "horizontal", "reverse")

See Also

ggpar, ggviolin, ggboxplot and ggstripchart.

Examples

# Load data
data("ToothGrowth")
df <- ToothGrowth

# Basic plot with summary statistics : mean_sd
# +++++++++++++++++++++++++++
ggdotplot(df, x = "dose", y = "len",
   add = "mean_sd")

# Change error.plot to "crossbar"
ggdotplot(df, x = "dose", y = "len",
 add = "mean_sd", add.params = list(width = 0.5),
 error.plot = "crossbar")


# Add box plot
ggdotplot(df, x = "dose", y = "len",
 add = "boxplot")

# Add violin + mean_sd
ggdotplot(df, x = "dose", y = "len",
 add = c("violin", "mean_sd"))


# Change colors
# +++++++++++++++++++++++++++
# Change fill and outline colors by groups: dose
# Use custom color palette
 ggdotplot(df, "dose", "len",
     add = "boxplot",
      color = "dose", fill = "dose",
      palette = c("#00AFBB", "#E7B800", "#FC4E07"))


# Plot with multiple groups
# +++++++++++++++++++++
# Change color by a second group : "supp"
ggdotplot(df, "dose", "len", fill = "supp", color = "supp",
    palette = c("#00AFBB", "#E7B800"))

ggpubr documentation built on Feb. 16, 2023, 7:18 p.m.