R/plot_befafter_colours.R
plot_befafter_colours.Rd
The 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_colours(
data,
xcol,
ycol,
match,
symsize = 3,
symthick = 1,
s_alpha = 1,
ColPal = "all_grafify",
ColSeq = TRUE,
ColRev = FALSE,
TextXAngle = 0,
fontsize = 20,
groups,
...
)
a data table object, e.g. data.frame or tibble.
name of the column containing the categorical variable to be plotted on the X axis.
name of the column containing the quantitative Y values.
name of the column with the matching variable to pass on to geom_line
.
size of symbols, default set to 3.
thickness of symbol border, default set to 1.
fractional opacity of symbols, default set to 1 (i.e. maximum opacity & zero transparency).
grafify colour palette to apply, default "all_grafify"; alternatives: "okabe_ito", "bright", "pale", "vibrant", "contrast", "muted" "dark", "light".
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
.
whether to reverse order of colour choice, default F (FALSE); can be set to T (TRUE).
orientation of text on X-axis; default 0 degrees. Change to 45 or 90 to remove overlapping text.
parameter of base_size
of fonts in theme_classic
, default set to size 20.
old argument name for match
; retained for backward compatibility.
any additional arguments to pass to ggplot2
geom_line.
This function returns a ggplot2
object of class "gg" and "ggplot".
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
.
More complex designs can also be plotted when used with facet_wrap
or facet_grid
.
#plot without legends if necessary
plot_befafter_colors(data = data_t_pdiff,
xcol = Condition, ycol = Mass,
match = Subject, s_alpha = .9, ColSeq = FALSE)+
guides(fill = "none",
colour = "none") #remove guides
#2way ANOVA design with randomised blocks
plot_befafter_colors(data = data_2w_Tdeath,
xcol = Genotype, ycol = PI,
match = Experiment) + facet_wrap("Time")