plot_scatterviolin {grafify}

Plot a scatter plot on a violin plot with two variables.

Description

There are 4 related functions that use geom_point to plot a categorical variable along the X axis.

1. plot_point_sd (mean & SD, SEM or CI95 error bars)

2. plot_scatterbar_sd (bar & SD, SEM or CI95 error bars)

3. plot_scatterbox (box & whiskers)

4. plot_scatterviolin (box & whiskers, violin)

Usage

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,
  bthick,
  vthick,
  bvthick,
  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 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.

facet

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

symsize

size of dots relative to binwidth used by geom_point. Default set to 3.

s_alpha

fractional opacity of symbols, default set to to 0.8 (i.e, 80% opacity). Set s_alpha = 0 to not show scatter plot.

b_alpha

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.

v_alpha

fractional opacity of violins, default set to 1.

bwid

width of boxplots; default 0.3.

vadjust

number to adjust the smooth/wigglyness of violin plot (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.

trim

set whether tips of violin plot should be trimmed at high/low data. Default trim = T, can be changed to F.

scale

set to "area" by default, can be changed to "count" or "width".

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.

Ylabels

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 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 boxplots; default = fontsize/22.

vthick

thickness (in 'pt' units) of violins; default = fontsize/22.

bvthick

thickness (in 'pt' units) of both violins and boxplots; 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_boxplot, ggplot2geom_point or ggplot2geom_violin.

Details

These functions take a data table, categorical X and numeric Y variables, and plot various geometries. The X variable is mapped to the fill aesthetic of symbols.

In plot_point_sd and plot_scatterbar_sd, default error bars are SD, which can be changed to SEM or CI95.

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 decides whether colours are picked by respecting the order in the palette or the most distant ones using colorRampPalette.

If you prefer a single colour for the graph, use the SingleColour argument.

Value

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

Examples

#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)