ggpubr (version 0.1.1)

ggscatter: Scatter plot

Description

Create a scatter plot.

Usage

ggscatter(data, x, y, color = "black", fill = "lightgray", palette = NULL, shape = 19, size = 2, point = TRUE, rug = FALSE, add = c("none", "reg.line", "loess"), add.params = list(), conf.int = FALSE, conf.int.level = 0.95, fullrange = FALSE, ellipse = FALSE, ellipse.level = 0.95, ellipse.type = "norm", ellipse.alpha = 0.1, mean.point = FALSE, mean.point.size = 2 * size, star.plot = FALSE, star.plot.lty = 1, star.plot.lwd = NULL, label = NULL, font.label = c(12, "plain"), label.select = NULL, repel = FALSE, label.rectangle = FALSE, cor.coef = FALSE, cor.method = "pearson", cor.coef.coord = c(NULL, NULL), cor.coef.size = 12, ggp = NULL, ggtheme = theme_classic2(), ...)

Arguments

data

a data frame

x, y

x and y variables for drawing.

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.

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").

ellipse.alpha

Alpha for ellipse specifying the transparency level of fill color. Use alpha = 0 for no fill color.

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").

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.

cor.coef

logical value. If TRUE, correlation coefficient with the p-value will be added to the plot.

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.

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.

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("mtcars")
df <- mtcars
df$cyl <- as.factor(df$cyl)
head(df[, c("wt", "mpg", "cyl")], 3)

# Basic plot
# +++++++++++++++++++++++++++
ggscatter(df, x = "wt", y = "mpg",
   color = "black", shape = 21, size = 3, # Points color, shape and size
   add = "reg.line",  # Add regressin line
   add.params = list(color = "blue", fill = "lightgray"), # Customize reg. line
   conf.int = TRUE, # Add confidence interval
   cor.coef = TRUE # Add correlation coefficient
   )

# loess method: local regression fitting
ggscatter(df, x = "wt", y = "mpg",
   add = "loess", conf.int = TRUE)


# Control point size by continuous variable values ("qsec")
ggscatter(df, x = "wt", y = "mpg",
   color = "#00AFBB", size = "qsec")


# Change colors
# +++++++++++++++++++++++++++
# Use custom color palette
# Add marginal rug
ggscatter(df, x = "wt", y = "mpg", color = "cyl",
   palette = c("#00AFBB", "#E7B800", "#FC4E07") )




# Add group ellipses and mean points
# Add stars
# +++++++++++++++++++
ggscatter(df, x = "wt", y = "mpg",
   color = "cyl", shape = "cyl",
   palette = c("#00AFBB", "#E7B800", "#FC4E07"),
   ellipse = TRUE, mean.point = TRUE,
   star.plot = TRUE)


# Textual annotation
# +++++++++++++++++
df$name <- rownames(df)
ggscatter(df, x = "wt", y = "mpg",
   color = "cyl", palette = c("#00AFBB", "#E7B800", "#FC4E07"),
   label = "name", repel = TRUE)