R/plot_scatterbar_sd.R
plot_scatterbar_sd.Rd
This function takes a data table, categorical X and numeric Y variables, and plots a graph with a jitterplot or scatterplot and bars showing means with SD error bars. It uses stat_summary
with geom = "bar"
, and geom_point
with position = position_jitter(width = 0.05)
.
plot_scatterbar_sd(
data,
xcol,
ycol,
symsize = 2.5,
symthick = 1,
bwid = 0.7,
ewid = 0.3,
jitter = 0,
b_alpha = 1,
s_alpha = 1,
ColPal = "all_grafify",
ColSeq = TRUE,
ColRev = FALSE,
TextXAngle = 0,
fontsize = 20
)
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.
size of point symbols, default set to 2.
thickness of symbol border, default set to 1.
width of bars, default set to 0.7.
width of error bars, default set to 0.3.
extent of jitter (scatter) of symbols, default is 0 (i.e. aligned symbols). To reduce symbol overlap, try 0.1-0.3 or higher.
fractional opacity of bars, default set to 1 (i.e. maximum opacity & zero transparency).
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.
This function returns a ggplot2
object of class "gg" and "ggplot".
Standard deviation (SD) is plotted through stat_summary
calculated using mean_sdl
from the ggplot2
package (get help with ?mean_sdl
), and 1x SD is plotted (fun.arg = list(mult = 1)
.
The X variable is mapped to the fill
aesthetic in the bar geometry and colour
aesthetic in geom_point
.
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
.
Three types of plots are available for scatter/jitter symbols and either bars+SD, boxplot or violin plots: plot_scatterbar_sd
, plot_scatterbox
and plot_scatterviolin
.
These are related to the three "dot" versions that use a different geometry for symbols: plot_dotbox
, plot_dotbar_sd
and plot_dotviolin
.
#with jitter
plot_scatterbar_sd(data = data_cholesterol,
xcol = Treatment, ycol = Cholesterol,
jitter = 0.1)
#white bars
plot_scatterbar_sd(data = data_cholesterol,
xcol = Treatment, ycol = Cholesterol,
b_alpha = 0)