Before-after style graph with a boxplot — plot_befafter

The plot_befafter_box, plot_befafter_colours, plot_befafter_colors and plot_befafter_shapes are for plotting matched data joined by lines. These functions take X and Y variables along with a data column with matching information (e.g. matched subjects or experiments etc.) and plot symbols matched by colour or shape.

plot_befafter_box(
  data,
  xcol,
  ycol,
  match,
  facet,
  PlotShapes = FALSE,
  symsize = 3,
  s_alpha = 0.8,
  b_alpha = 1,
  bwid = 0.4,
  jitter = 0.1,
  TextXAngle = 0,
  LogYTrans,
  LogYBreaks = waiver(),
  LogYLabels = waiver(),
  LogYLimits = NULL,
  facet_scales = "fixed",
  fontsize = 20,
  symthick,
  bthick,
  ColPal = c("okabe_ito", "all_grafify", "bright", "contrast", "dark", "fishy", "kelly",
    "light", "muted", "pale", "r4", "safe", "vibrant"),
  ColSeq = TRUE,
  ColRev = FALSE,
  SingleColour = "NULL",
  ...
)

Arguments

data: a data table object, e.g. data.frame or tibble.
xcol: name of the column containing the categorical variable to be plotted on the X axis.
ycol: name of the column containing the quantitative Y values.
match: name of the column with the grouping variable to pass on to geom_line.
facet: add another variable from the data table to create faceted graphs using ggplot2facet_wrap.
PlotShapes: logical TRUE or FALSE (default = FALSE) if the shape of the symbol is to be mapped to the match variable. Note that only 25 shapes allowed.
symsize: size of symbols, default set to 3.
s_alpha: fractional opacity of symbols, default set to 0.8 (i.e., 80% opacity).
b_alpha: fractional opacity of boxes, default set to 1.
bwid: width of boxplots; default 0.4.
jitter: extent of jitter (scatter) of symbols, default is 0.1. Increase to reduce symbol overlap, set to 0 for aligned symbols.
TextXAngle: orientation of text on X-axis; default 0 degrees. Change to 45 or 90 to remove overlapping text.
LogYTrans: transform Y axis into "log10" or "log2"
LogYBreaks: argument for ggplot2[scale_y_continuous] for Y axis breaks on log scales, default is waiver(), or provide a vector of desired breaks.
LogYLabels: argument for ggplot2[scale_y_continuous] for Y axis labels on log scales, default is waiver(), or provide a vector of desired labels.
LogYLimits: a vector of length two specifying the range (minimum and maximum) of the Y axis.
facet_scales: whether or not to fix scales on X & Y axes for all facet facet graphs. Can be fixed (default), free, free_y or free_x (for Y and X axis one at a time, respectively).
fontsize: parameter of base_size of fonts in theme_classic, default set to size 20.
symthick: size (in 'pt' units) of outline of symbol lines (stroke), default = fontsize/22.
bthick: thickness (in 'pt' units) of lines and boxes lines; default = fontsize/22.
ColPal: grafify colour palette to apply, default "okabe_ito"; see graf_palettes for available palettes.
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 within the selected palette, default F (FALSE); can be set to T (TRUE).
SingleColour: a colour hexcode (starting with #), a number between 1-154, or names of colours from grafify or base R palettes to fill along X-axis aesthetic. Accepts any colour other than "black"; use grey_lin11, which is almost black.
...: any additional arguments to pass to ggplot2geom_line, ggplot2geom_point, or ggplot2facet_wrap.

Value

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

Details

Use plot_befafter_box to also get a boxplot with matched data. In this function, the categorical variable along X axis is mapped to the fill-colour aesthetic.

The default is a plot without matching shapes. Change the PlotShapes argument to TRUE for plot similar to plot_befafter_shapes. Note that with PlotShapes = TRUE the colour of symbols will always be black and the X-axis variable is mapped to the fill colour of boxplots.

Note that only 25 shapes are available, and there will be errors with plot_befafter_shapes when there are fewer than 25 matched observations; instead use default (PlotShapes = FALSE).

Add another variable to make faceted graphs with the facet argument.

Colours can be changed using ColPal, ColRev or ColSeq arguments. 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 decides whether colours are picked by respecting the order in the palette or the most distant ones using colorRampPalette.

To plot a graph with a single colour along the X axis variable, use the SingleColour argument.

Examples

#plot without legends if necessary
plot_befafter_box(data = data_t_pdiff, 
xcol = Condition, ycol = Mass, 
match = Subject)

#with PlotShapes = TRUE
plot_befafter_box(data = data_t_pdiff, 
xcol = Condition, ycol = Mass, 
match = Subject, PlotShapes = TRUE)

#2way ANOVA design with randomised blocks
plot_befafter_box(data = data_2w_Tdeath, 
xcol = Time2, ycol = PI, 
match = Experiment, facet = Genotype)