R: Stripcharts

ggstripchart {ggpubr} | R Documentation

## Stripcharts

### Description

Create a stripchart, also known as one dimensional scatter plots. These plots are suitable compared to box plots when sample sizes are small.

### Usage

    ggstripchart(data, x, y, combine = FALSE, merge = FALSE, color = "black",
      fill = "white", palette = NULL, title = NULL, xlab = NULL,
      ylab = NULL, facet.by = NULL, panel.labs = NULL,
      short.panel.labs = TRUE, shape = 19, size = NULL, select = NULL,
      remove = NULL, order = NULL, add = "mean_se", add.params = list(),
      error.plot = "pointrange", label = NULL, font.label = list(size = 11,
      color = "black"), label.select = NULL, repel = FALSE,
      label.rectangle = FALSE, jitter = 0.2,
      position = position_jitter(jitter), ggtheme = theme_pubr(), ...)

### Arguments

`data` | a data frame
`x` | character string containing the name of x variable.
`y` | character vector containing one or more variables to plot
`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` | outline color.
`fill` | fill color.
`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".
`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.
`shape` | point shape
`size` | Numeric value (e.g.: size = 1). change the size of points and outlines.
`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` | the name of the column containing point labels. Can be also a character vector with length = nrow(data).
`font.label` | a list which can contain the combination of the following elements: the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of labels. For example font.label = list(size = 14, face = "bold", color ="red"). To specify only the size and the style, use font.label = list(size = 14, face = "plain").
`label.select` | can be of two formats: a character vector specifying some labels to show. a list containing one or the combination of the following components: `top.up` and `top.down`: to display the labels of the top up/down points. For example, `label.select = list(top.up = 10, top.down = 4)`. `criteria`: to filter, for example, by x and y variabes values, use this: `label.select = list(criteria = "`y` > 2 & `y` < 5 & `x` %in% c('A', 'B')")`.
`repel` | a logical value, whether to use ggrepel to avoid overplotting text labels or not.
`label.rectangle` | logical value. If TRUE, add rectangle underneath the text, making it easier to read.
`jitter` | the amount of jitter.
`position` | position adjustment, either as a string, or the result of a call to a position adjustment function. Used to adjust position for multiple groups.
`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 `geom_jitter`, `ggpar` and `facet`.

### 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`, `ggviolin`, `ggdotplot` and `ggboxplot`.

### Examples

    # Load data
    data("ToothGrowth")
    df <- ToothGrowth

    # Basic plot with summary statistics: mean_se
    # +++++++++++++++++++++++++++
    # Change point shapes by groups: "dose"
    ggstripchart(df, x = "dose", y = "len",
       shape = "dose", size = 3,
       add = "mean_se")

    # Use mean_sd
    # Change error.plot to "crossbar"
    ggstripchart(df, x = "dose", y = "len",
       shape = "dose", size = 3,
       add = "mean_sd", add.params = list(width = 0.5),
       error.plot = "crossbar")

    # Add summary statistics
    # ++++++++++++++++++++++++++

    # Add box plot
    ggstripchart(df, x = "dose", y = "len",
     shape = "dose", add = "boxplot")

    # Add violin + mean_sd
    ggstripchart(df, x = "dose", y = "len",
     shape = "dose", add = c("violin", "mean_sd"))

    # Change colors
    # +++++++++++++++++++++++++++
    # Change colors by groups: dose
    # Use custom color palette
     ggstripchart(df, "dose", "len",  shape = "dose",
       color = "dose", palette = c("#00AFBB", "#E7B800", "#FC4E07"),
       add = "mean_sd")

    # Plot with multiple groups
    # +++++++++++++++++++++
    # Change shape and color by a second group : "supp"
    ggstripchart(df, "dose", "len", shape = "supp",
      color = "supp", palette = c("#00AFBB", "#E7B800"))

    # Adjust point position
    ggstripchart(df, "dose", "len", shape = "supp",
      color = "supp", palette = c("#00AFBB", "#E7B800"),
      position = position_dodge(0.8) )

    # You can also use position_jitterdodge()
    # but fill aesthetic is required
    ggstripchart(df, "dose", "len",  shape = "supp",
       color = "supp", palette = c("#00AFBB", "#E7B800"),
       position = position_jitterdodge() )

    # Add boxplot
    ggstripchart(df, "dose", "len", shape = "supp",
     color = "supp", palette = c("#00AFBB", "#E7B800"),
     add = "boxplot", add.params = list(color = "black") )

[Package ggpubr version 0.1.6 Index]