R: Bar plot

ggbarplot {ggpubr} | R Documentation

## Bar plot

### Description

Create a bar plot.

### Usage

    ggbarplot(data, x, y, 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 = "errorbar", label = FALSE, lab.col = "black",
      lab.size = 4, lab.pos = c("out", "in"), lab.vjust = NULL,
      lab.hjust = NULL, lab.nb.digits = NULL, sort.val = c("none", "desc",
      "asc"), sort.by.groups = TRUE, top = Inf, position = position_stack(),
      ggtheme = theme_pubr(), ...)

### Arguments

`data` | a data frame
`x, y` | x and y variables for drawing.
`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, ....
`label` | specify whether to add labels on the bar plot. Allowed values are: logical value: If TRUE, y values is added as labels on the bar plot character vector: Used as text labels; must be the same length as y.
`lab.col, lab.size` | text color and size for labels.
`lab.pos` | character specifying the position for labels. Allowed values are "out" (for outside) or "in" (for inside). Ignored when lab.vjust != NULL.
`lab.vjust` | numeric, vertical justification of labels. Provide negative value (e.g.: -0.4) to put labels outside the bars or positive value to put labels inside (e.g.: 2).
`lab.hjust` | numeric, horizontal justification of labels.
`lab.nb.digits` | integer indicating the number of decimal places (round) to be used.
`sort.val` | a string specifying whether the value should be sorted. Allowed values are "none" (no sorting), "asc" (for ascending) or "desc" (for descending).
`sort.by.groups` | logical value. If TRUE the data are sorted by groups. Used only when sort.val != "none".
`top` | a numeric value specifying the number of top elements to be shown.
`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
    df <- data.frame(dose=c("D0.5", "D1", "D2"),
       len=c(4.2, 10, 29.5))
    print(df)

    # Basic plot with label outsite
    # +++++++++++++++++++++++++++
    ggbarplot(df, x = "dose", y = "len",
      label = TRUE, label.pos = "out")

    # Change width
    ggbarplot(df, x = "dose", y = "len", width = 0.5)

    # Change the plot orientation: horizontal
    ggbarplot(df, "dose", "len", orientation = "horiz")

    # Change the default order of items
    ggbarplot(df, "dose", "len",
       order = c("D2", "D1", "D0.5"))

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

    # Change fill and outline color
    # add labels inside bars
    ggbarplot(df, "dose", "len",
     fill = "steelblue", color = "steelblue",
     label = TRUE, lab.pos = "in", lab.col = "white")

    # Change colors by groups: dose
    # Use custom color palette
     ggbarplot(df, "dose", "len", color = "dose",
       palette = c("#00AFBB", "#E7B800", "#FC4E07"))

    # Change fill and outline colors by groups
     ggbarplot(df, "dose", "len",
       fill = "dose", color = "dose",
       palette = c("#00AFBB", "#E7B800", "#FC4E07"))

    # 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 color by a second group: "supp"
    # Add labels inside bars
    ggbarplot(df2, "dose", "len",
      fill = "supp", color = "supp", palette = "Paired",
      label = TRUE, lab.col = "white", lab.pos = "in")

    # Change position: Interleaved (dodged) bar plot
    ggbarplot(df2, "dose", "len",
      fill = "supp", color = "supp", palette = "Paired",
      label = TRUE,
      position = position_dodge(0.9))

    # 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
    ggbarplot(df3, x = "dose", y = "len")

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

    # Add error bars: mean_se
    # (other values include: mean_sd, mean_ci, median_iqr, ....)
    # Add labels
    ggbarplot(df3, x = "dose", y = "len",
     add = "mean_se", label = TRUE, lab.vjust = -1.6)

    # Use only "upper_errorbar"
    ggbarplot(df3, x = "dose", y = "len",
     add = "mean_se", error.plot = "upper_errorbar")

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

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

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

    # Multiple groups with error bars and jitter point
    ggbarplot(df3, x = "dose", y = "len", color = "supp",
     add = "mean_se", palette = c("#00AFBB", "#E7B800"),
     position = position_dodge())

[Package ggpubr version 0.1.6 Index]