ggerrorplot | R Documentation |
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(), ... )
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 |
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. |
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(). |
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")
ggpar
, ggline
# 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))
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