Plot a before-after plot with lines joining colour-matched symbols.

Source: R/plot_befafter_colours.R

One of 3 related functions to plot matching data joined by lines. The variable containing information for matching (e.g. matched subjects or experiments etc.) is passed to the match argument.

  1. plot_befafter_colours or plot_befafter_colors,

  2. plot_befafter_shapes

  3. plot_befafter_box

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

plot_befafter_colors(
  data,
  xcol,
  ycol,
  match,
  facet,
  Boxplot = FALSE,
  symsize = 3,
  s_alpha = 1,
  jitter = 0.1,
  bwid = 0.4,
  TextXAngle = 0,
  LogYTrans,
  LogYBreaks = waiver(),
  LogYLabels = waiver(),
  LogYLimits = NULL,
  facet_scales = "fixed",
  fontsize = 20,
  symthick,
  bthick,
  lthick,
  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 matching variable to pass on to geom_line.

facet

add another variable from the data table to create faceted graphs using ggplot2facet_wrap.

Boxplot

logical TRUE/FALSE, whether to show box and whisker plot or not (default is FALSE)

symsize

size of symbols, default set to 3.

s_alpha

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

jitter

extent of jitter (scatter) of symbols, default is 0.1. Increase to reduce symbol overlap, set to 0 for aligned symbols.

bwid

width of boxplots; default 0.4.

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 boxes; default = (fontsize)/22.

lthick

thickness (in 'pt' units) of lines; default = (fontsize/1.2)/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 or ggplot2geom_point.

Value

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

Details

In plot_befafter_colours/plot_befafter_colors and plot_befafter_shapes setting Boxplot = TRUE will also plot a box and whiskers plot.

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 plot_befafter_colours instead.

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.

The resulting ggplot2 graph can take additional geometries or other layers.

Examples

#plot without legends if necessary
plot_befafter_colours(data = data_t_pdiff, 
xcol = Condition, ycol = Mass, 
match = Subject, s_alpha = .9, ColSeq = FALSE)+
guides(fill = "none", 
colour = "none") #remove guides

#plot with boxplot
plot_befafter_colours(data = data_t_pdiff, 
xcol = Condition, ycol = Mass, 
match = Subject, s_alpha = .9, ColSeq = FALSE,
Boxplot = TRUE)+
guides(fill = "none", 
colour = "none") #remove guides