ggpubr (version 0.1.1)

ggdotplot: Dot plot

Description

Create a dot plot.

Usage

ggdotplot(data, x, y, color = "black", fill = "lightgray", palette = NULL, size = NULL, select = NULL, order = NULL, add = "mean_se", add.params = list(), error.plot = "pointrange", ggtheme = theme_classic2(), ...)

Arguments

data

a data frame

x, y

x and y variables for drawing.

color, fill

outline and fill 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".

size

Numeric value (e.g.: size = 1). change the size of points and outlines.

select

character vector specifying which items to display.

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_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, ....

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.

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

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"))