Visualizing Error

Visualizing error.

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

data: a data frame
x, y: x and y variables for drawing.
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 desc_statby for more details.
numeric.x.axis: logical. If TRUE, x axis will be treated as numeric. Default is FALSE.
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, 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.
width: numeric value between 0 and 1 specifying box width.
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.
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. Considered only when x axis is a factor variable.
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, ....
ci: the percent range of the confidence interval (default is 0.95).
position: Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use 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.
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 be passed to 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")

Examples


# Data: ToothGrowth data set we'll be used.
df<- ToothGrowth
head(df, 10)
#>     len supp dose
#> 1   4.2   VC  0.5
#> 2  11.5   VC  0.5
#> 3   7.3   VC  0.5
#> 4   5.8   VC  0.5
#> 5   6.4   VC  0.5
#> 6  10.0   VC  0.5
#> 7  11.2   VC  0.5
#> 8  11.2   VC  0.5
#> 9   5.2   VC  0.5
#> 10  7.0   VC  0.5

# 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")
#> Warning: The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
#> ℹ Please use the `fun` argument instead.
#> ℹ The deprecated feature was likely used in the ggpubr package.
#>   Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
#> Warning: The `fun.ymin` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
#> ℹ Please use the `fun.min` argument instead.
#> ℹ The deprecated feature was likely used in the ggpubr package.
#>   Please report the issue at <https://github.com/kassambara/ggpubr/issues>.
#> Warning: The `fun.ymax` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.
#> ℹ Please use the `fun.max` argument instead.
#> ℹ The deprecated feature was likely used in the ggpubr package.
#>   Please report the issue at <https://github.com/kassambara/ggpubr/issues>.


# 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")
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.


# 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))

Arguments

Details

See also

Examples