Plot a point as mean with SD error bars using two variables.

Source: R/plot_point_sd.R

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)

plot_point_sd(
  data,
  xcol,
  ycol,
  facet,
  ErrorType = "SD",
  symsize = 3.5,
  s_alpha = 1,
  symshape = 22,
  all_alpha = 0.3,
  all_size = 2.5,
  all_shape = 1,
  all_jitter = 0,
  ewid = 0.2,
  TextXAngle = 0,
  LogYTrans,
  LogYBreaks = waiver(),
  LogYLabels = waiver(),
  LogYLimits = NULL,
  facet_scales = "fixed",
  fontsize = 20,
  symthick,
  ethick,
  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 (without quotes) with a X variable (will be forced to be a factor/categorical variable).

ycol

name of the column (without quotes) with quantitative Y variable.

facet

add another variable (without quotes) from the data table to create faceted graphs using facet_wrap.

ErrorType

select the type of error bars to display. Default is "SD" (standard deviation). Other options are "SEM" (standard error of the mean) and "CI95" (95% confidence interval based on t distributions).

symsize

size of point symbols, default set to 3.5.

s_alpha

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

symshape

The mean is shown with symbol of the shape number 22 (default, filled square). Pick a number between 21-25 to pick a different type of symbol from ggplot2.

all_alpha

fractional opacity of all data points (default = 0.3). Set to non-zero value if you would like all data points plotted in addition to the mean.

all_size

size of symbols of all data points, if shown (default = 2.5).

all_shape

all data points are shown with symbols of the shape number 1 (default, transparent circle). Pick a number between 0-25 to pick a different type of symbol from ggplot2.

all_jitter

reduce overlap of all data points, if shown, by setting a value between 0-1 (default = 0).

ewid

width of error bars, default set to 0.2.

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" (in quotes).

LogYBreaks

argument for scale_y_continuous for Y axis breaks on log scales, default is waiver(), or provide a vector of desired breaks.

LogYLabels

argument for 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

thickness of symbol border, default set to fontsize/22.

ethick

thickness of error bar lines; default fontsize/22.

ColPal

grafify colour palette to apply (in quotes), 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 #, e.g., "#E69F00"), 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 stat_summary.

Value

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

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 (logical TRUE/FALSE) decides whether colours are picked by respecting the order in the palette or the most distant ones using colorRampPalette.

If there are many groups along the X axis and you prefer a single colour for the graph,use the SingleColour argument.

Examples

#Basic usage
plot_point_sd(data = data_doubling_time, 
xcol = Student, ycol = Doubling_time)