This function takes a data table, X and Y variables, and plots a graph with a scatter plot and box and whiskers using geom_boxplot and geom_point geometries. The boxplot shows IQR and whiskers depict 1.5*IQR. Note that geom_boxplot option for outliers is set to outlier.alpha = 0. The X variable is mapped to the fill aesthetic in both boxplot and symbols, and its colour can be changed using ColPal option. Colours can be changed using ColPal, ColRev or ColSeq arguments. Colours available can be seen quickly with plot_grafify_palette. ColPal can be one of the following: "okabe_ito", "dark", "light", "bright", "pale", "vibrant, "muted" or "contrast". ColRev (logical TRUE/FALSE) decides whether colours are chosen from first-to-last or last-to-first from within the chosen palette. ColSeq (logical TRUE/FALSE) decides whether colours are picked by respecting the order in the palette or the most distant ones using colorRampPalette.

plot_scatterbox(
  data,
  xcol,
  ycol,
  symsize = 2.5,
  symthick = 1,
  jitter = 0,
  b_alpha = 1,
  s_alpha = 1,
  ColPal = "all_grafify",
  ColSeq = TRUE,
  ColRev = FALSE,
  TextXAngle = 0,
  fontsize = 20,
  ...
)

Arguments

data

a data table object, e.g. data.frame or tibble.

xcol

name of the column to plot on X axis. This should be a categorical variable.

ycol

name of the column to plot on quantitative Y axis. This should be a quantitative variable.

symsize

size of symbols used by geom_point. Default set to 2.5, increase/decrease as needed.

symthick

thickness of symbol border (stroke parameter of geom_point), default set to 1.

jitter

extent of jitter (scatter) of symbols, default is 0 (i.e. aligned symbols). To reduce symbol overlap, try 0.1-0.3 or higher.

b_alpha

fractional opacity of boxplot, default set to 1 (i.e. maximum opacity & zero transparency).

s_alpha

fractional opacity of symbols, default set to 1 (i.e. maximum opacity & zero transparency).

ColPal

grafify colour palette to apply, default "all_grafify"; alternatives: "okabe_ito", "bright", "pale", "vibrant", "contrast", "muted" "dark", "light".

ColSeq

logical TRUE or FALSE. Default TRUE for sequential colours from chosen palette. Set to FALSE for distant colours, which will be applied using scale_fill_grafify2.

ColRev

whether to reverse order of colour choice, default F (FALSE); can be set to T (TRUE).

TextXAngle

orientation of text on X-axis; default 0 degrees. Change to 45 or 90 to remove overlapping text.

fontsize

parameter of base_size of fonts in theme_classic, default set to size 20.

...

any additional arguments to pass to ggplot2geom_boxplot.

Value

This function returns a ggplot2 object of class "gg" and "ggplot".

Details

The size of symbols can be adjusted using symsize set to 1 by default. Transparency of boxplot and symbols can be set independently with b_alpha and s_alpha, respectively.

Three types of plots are available for scatter/jitter symbols and either bars+SD, boxplot or violin plots: plot_scatterbar_sd, plot_scatterbox and plot_scatterviolin. These are related to the three "dot" versions that use a different geometry for symbols: plot_scatterbox, plot_dotbar_sd and plot_dotviolin.

Examples

plot_scatterbox(data = data_cholesterol, 
xcol = Treatment, ycol = Cholesterol)


#with jitter
plot_scatterbox(data = data_cholesterol, 
xcol = Treatment, ycol = Cholesterol, jitter = 0.1)