R: Visualizing Error

ggerrorplot {ggpubr} | R Documentation

## Visualizing Error

### Description

Visualizing error.

### Usage

    ggerrorplot(data, x, y, desc_stat = "mean_se", 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",
      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_mad", "median_range"; see `desc_statby` for more details.
`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.
`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, ....
`position` | Position adjustment, either as a string, or the result of a call to a position adjustment function.
`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")

### See Also

`ggpar`, `ggline`

### 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))

[Package ggpubr version 0.1.6 Index]