There are three types of
plot_dot_ functions that plot "dots" as data symbols plotted with
geom_dotplot geometry. Variants can show summary and data distributions as bar and SD errors (plot_dotbar_sd; or SEM or CI95 error bars), box and whisker plots (plot_dotbox) or violin and box & whiskers plots (plot_dotviolin). They all take a data table, a categorical X variable and a numeric Y variable.
plot_scatterviolin( data, xcol, ycol, facet, symsize = 3, s_alpha = 0.8, b_alpha = 0, v_alpha = 1, bwid = 0.3, vadjust = 1, jitter = 0.1, trim = TRUE, scale = "width", TextXAngle = 0, LogYTrans, LogYBreaks = waiver(), Ylabels = waiver(), LogYLimits = NULL, facet_scales = "fixed", fontsize = 20, symthick, bvthick, ColPal = c("okabe_ito", "all_grafify", "bright", "contrast", "dark", "fishy", "kelly", "light", "muted", "pale", "r4", "safe", "vibrant"), ColSeq = TRUE, ColRev = FALSE, SingleColour = "NULL", ... )
a data table object, e.g. data.frame or tibble.
name of the column to plot on X axis. This should be a categorical variable.
name of the column to plot on quantitative Y axis. This should be a quantitative variable.
add another variable from the data table to create faceted graphs using
size of dots relative to
binwidth used by
geom_point. Default set to 3.
fractional opacity of symbols, default set to to 0.8 (i.e, 80% opacity). Set
s_alpha = 0 to not show scatter plot.
fractional opacity of boxplots. Default is set to 0, which results in white boxes inside violins. Change to any value >0 up to 1 for different levels of transparency.
fractional opacity of violins, default set to 1.
width of boxplots; default 0.3.
number to adjust the smooth/wigglyness of violin plot (default set to 1).
extent of jitter (scatter) of symbols, default is 0 (i.e. aligned symbols). To reduce symbol overlap, try 0.1-0.3 or higher.
set whether tips of violin plot should be trimmed at high/low data. Default
trim = T, can be changed to F.
set to "area" by default, can be changed to "count" or "width".
orientation of text on X-axis; default 0 degrees. Change to 45 or 90 to remove overlapping text.
transform Y axis into "log10" or "log2"
ggplot2[scale_y_continuous] for Y axis breaks on log scales, default is
waiver(), or provide a vector of desired breaks.
ggplot2[scale_y_continuous] for Y axis labels on log scales, default is
waiver(), or provide a vector of desired labels.
a vector of length two specifying the range (minimum and maximum) of the Y axis.
whether or not to fix scales on X & Y axes for all graphs. Can be
free_x (for Y and X axis one at a time, respectively).
base_size of fonts in
theme_classic, default set to size 20.
size (in 'pt' units) of outline of symbol lines (
stroke), default =
thickness (in 'pt' units) of both violin and boxplot lines; default =
grafify colour palette to apply, default "okabe_ito"; see
graf_palettes for available palettes.
logical TRUE or FALSE. Default TRUE for sequential colours from chosen palette. Set to FALSE for distant colours, which will be applied using
whether to reverse order of colour within the selected palette, default F (FALSE); can be set to T (TRUE).
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
This function returns a
ggplot2 object of class "gg" and "ggplot".
plot_scatter_ variants show data symbols using the
geom_point geometry. These are plot_scatterbar_sd (or SEM or CI95 error bars), plot_scatterbox and plot_scatterviolin. Overplotting in
plot_scatter variants can be reduced with the
The X variable is mapped to the
fill aesthetic of dots, symbols, bars, boxes and violins.
Colours can be changed using
ColSeq arguments. Colours available can be seen quickly with
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
If you prefer a single colour for the graph, use the
#plot without jitter plot_scatterviolin(data = data_t_pdiff, xcol = Condition, ycol = Mass, symsize = 2, trim = FALSE) #no symbols plot_scatterviolin(data = data_t_pdiff, xcol = Condition, ycol = Mass, s_alpha = 0, symsize = 2, trim = FALSE) #single colour along X plot_scatterviolin(data = data_t_pdiff, xcol = Condition, ycol = Mass, SingleColour = "pale_blue", s_alpha = 0, symsize = 2, trim = FALSE)