ggpubr (version 0.1.1)

ggline: Line plot

Description

Create a line plot.

Usage

ggline(data, x, y, group = 1, color = "black", palette = NULL, linetype = "solid", plot_type = c("b", "l", "p"), size = 0.5, shape = 19, select = NULL, order = NULL, add = "none", add.params = list(), error.plot = "errorbar", ggtheme = theme_classic2(), ...)

Arguments

data

a data frame

x, y

x and y variables for drawing.

group

grouping variable to connect points by line. Allowed values are 1 (for one line, one group) or a character vector specifying the name of the grouping variable (case of multiple lines).

color

line 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".

linetype

line type.

plot_type

plot type. Allowed values are one of "b" for both line and point; "l" for line only; and "p" for point only. Default is "b".

size

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

shape

point shapes.

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, ggbarplot

Examples

# Data
df <- data.frame(dose=c("D0.5", "D1", "D2"),
   len=c(4.2, 10, 29.5))
print(df)

# Basic plot
# +++++++++++++++++++++++++++
ggline(df, x = "dose", y = "len")


# Plot with multiple groups
# +++++++++++++++++++++

# Create some data
df2 <- data.frame(supp=rep(c("VC", "OJ"), each=3),
   dose=rep(c("D0.5", "D1", "D2"),2),
   len=c(6.8, 15, 33, 4.2, 10, 29.5))
print(df2)

# Plot "len" by "dose" and
# Change line types and point shapes by a second groups: "supp"
ggline(df2, "dose", "len",
  linetype = "supp", shape = "supp")


# Change colors
# +++++++++++++++++++++

# Change color by group: "supp"
# Use custom color palette
ggline(df2, "dose", "len",
   linetype = "supp", shape = "supp",
   color = "supp", palette = c("#00AFBB", "#E7B800"))


# Add points and errors
# ++++++++++++++++++++++++++

# Data: ToothGrowth data set we'll be used.
df3 <- ToothGrowth
head(df3, 10)

# It can be seen that for each group we have
# different values
ggline(df3, x = "dose", y = "len")

# Visualize the mean of each group
ggline(df3, x = "dose", y = "len",
 add = "mean")

# Add error bars: mean_se
# (other values include: mean_sd, mean_ci, median_iqr, ....)
# Add labels
ggline(df3, x = "dose", y = "len", add = "mean_se")

# Change error.plot to "pointrange"
ggline(df3, x = "dose", y = "len",
 add = "mean_se", error.plot = "pointrange")

# Add jitter points and errors (mean_se)
ggline(df3, x = "dose", y = "len",
 add = c("mean_se", "jitter"))

# Add dot and errors (mean_se)
ggline(df3, x = "dose", y = "len",
 add = c("mean_se", "dotplot"), color = "steelblue")

# Add violin and errors (mean_se)
ggline(df3, x = "dose", y = "len",
 add = c("mean_se", "violin"), color = "steelblue")

# Multiple groups with error bars
# ++++++++++++++++++++++

ggline(df3, x = "dose", y = "len", color = "supp",
 add = "mean_se", palette = c("#00AFBB", "#E7B800"))

# Add jitter
ggline(df3, x = "dose", y = "len", color = "supp",
 add = c("mean_se", "jitter"), palette = c("#00AFBB", "#E7B800"))

# Add dot plot
ggline(df3, x = "dose", y = "len", color = "supp",
 add = c("mean_se", "dotplot"), palette = c("#00AFBB", "#E7B800"))