1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
|
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggerrorplot.R
\name{ggerrorplot}
\alias{ggerrorplot}
\title{Visualizing Error}
\usage{
ggerrorplot(
data,
x,
y,
desc_stat = "mean_se",
numeric.x.axis = FALSE,
combine = FALSE,
merge = FALSE,
color = "black",
fill = "white",
palette = NULL,
size = NULL,
width = NULL,
title = NULL,
xlab = NULL,
ylab = NULL,
facet.by = NULL,
panel.labs = NULL,
short.panel.labs = TRUE,
select = NULL,
remove = NULL,
order = NULL,
add = "none",
add.params = list(),
error.plot = "pointrange",
ci = 0.95,
position = position_dodge(),
ggtheme = theme_pubr(),
...
)
}
\arguments{
\item{data}{a data frame}
\item{x, y}{x and y variables for drawing.}
\item{desc_stat}{descriptive statistics to be used for visualizing errors. Default value is "mean_se".
Allowed values are one of , "mean", "mean_se", "mean_sd", "mean_ci", "mean_range",
"median", "median_iqr", "median_hilow", "median_q1q3", "median_mad", "median_range"; see \code{\link{desc_statby}} for more details.}
\item{numeric.x.axis}{logical. If TRUE, x axis will be treated as numeric. Default is FALSE.}
\item{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.}
\item{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.}
\item{color, fill}{outline and fill colors.}
\item{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".}
\item{size}{Numeric value (e.g.: size = 1). change the size of points and
outlines.}
\item{width}{numeric value between 0 and 1 specifying box width.}
\item{title}{plot main title.}
\item{xlab}{character vector specifying x axis labels. Use xlab = FALSE to
hide xlab.}
\item{ylab}{character vector specifying y axis labels. Use ylab = FALSE to
hide ylab.}
\item{facet.by}{character vector, of length 1 or 2, specifying grouping
variables for faceting the plot into multiple panels. Should be in the data.}
\item{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") ).}
\item{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.}
\item{select}{character vector specifying which items to display.}
\item{remove}{character vector specifying which items to remove from the plot.}
\item{order}{character vector specifying the order of items. Considered only when x axis is a factor variable.}
\item{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.}
\item{add.params}{parameters (color, shape, size, fill, linetype) for the
argument 'add'; e.g.: add.params = list(color = "red").}
\item{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, ....}
\item{ci}{the percent range of the confidence interval (default is 0.95).}
\item{position}{Position adjustment, either as a string naming the adjustment
(e.g. \code{"jitter"} to use \code{position_jitter}), or the result of a call to a
position adjustment function. Use the latter if you need to change the
settings of the adjustment.}
\item{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(), ....}
\item{...}{other arguments to be passed to be passed to ggpar().}
}
\description{
Visualizing error.
}
\details{
The plot can be easily customized using the function ggpar(). Read
?ggpar for changing: \itemize{ \item main title and axis labels: main,
xlab, ylab \item axis limits: xlim, ylim (e.g.: ylim = c(0, 30)) \item axis
scales: xscale, yscale (e.g.: yscale = "log2") \item color palettes:
palette = "Dark2" or palette = c("gray", "blue", "red") \item legend title,
labels and position: legend = "right" \item plot orientation : orientation
= c("vertical", "horizontal", "reverse") }
}
\examples{
# Data: ToothGrowth data set we'll be used.
df<- ToothGrowth
head(df, 10)
# Plot mean_se
ggerrorplot(df, x = "dose", y = "len")
# Change desc_stat to mean_sd
# (other values include: mean_sd, mean_ci, median_iqr, ....)
# Add labels
ggerrorplot(df, x = "dose", y = "len",
desc_stat = "mean_sd")
# Change error.plot to "errorbar" and add mean point
# Visualize the mean of each group
ggerrorplot(df, x = "dose", y = "len",
add = "mean", error.plot = "errorbar")
# Horizontal plot
ggerrorplot(df, x = "dose", y = "len",
add = "mean", error.plot = "errorbar",
orientation = "horizontal")
# Change error.plot to "crossbar"
ggerrorplot(df, x = "dose", y = "len",
error.plot = "crossbar", width = 0.5)
# Add jitter points and errors (mean_se)
ggerrorplot(df, x = "dose", y = "len",
add = "jitter")
# Add dot and errors (mean_se)
ggerrorplot(df, x = "dose", y = "len",
add = "dotplot")
# Multiple groups with error bars and jitter point
ggerrorplot(df, x = "dose", y = "len",
color = "supp", palette = "Paired",
error.plot = "pointrange",
position = position_dodge(0.5))
}
\seealso{
\code{\link{ggpar}}, \code{\link{ggline}}
}
|
