`R/plot_dotbar_sd.R`

`plot_dotbar_sd.Rd`

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_dotbar_sd(
data,
xcol,
ycol,
facet,
ErrorType = "SD",
dotsize = 1.5,
d_alpha = 0.8,
b_alpha = 1,
bwid = 0.5,
ewid = 0.2,
TextXAngle = 0,
LogYTrans,
LogYBreaks = waiver(),
LogYLabels = waiver(),
LogYLimits = NULL,
facet_scales = "fixed",
fontsize = 20,
dotthick,
bthick,
ColPal = c("okabe_ito", "all_grafify", "bright", "contrast", "dark", "fishy", "kelly",
"light", "muted", "pale", "r4", "safe", "vibrant"),
ColSeq = TRUE,
ColRev = FALSE,
SingleColour = "NULL",
...
)
```

- 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

`ggplot2`

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).

- dotsize
size of dots relative to binwidth used by

`geom_dotplot`

. Default set to 1.5, increase/decrease as needed.- d_alpha
fractional opacity of dots, default set to 0.8 (i.e., 80% opacity).

- b_alpha
fractional opacity of bars, default set to 1.

- bwid
width of bars; default 0.5.

- 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"

- LogYBreaks
argument for

`ggplot2[scale_y_continuous]`

for Y axis breaks on log scales, default is`waiver()`

, or provide a vector of desired breaks.- LogYLabels
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 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.- dotthick
thickness of dot border (

`stroke`

parameter of`geom_dotplot`

), default set to`fontsize`

/22.- bthick
thickness (in 'pt' units) of bar and error bar lines; 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

`ggplot2`

geom_dotplot.

This function returns a `ggplot2`

object of class "gg" and "ggplot".

Related `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 `jitter`

argument.

The X variable is mapped to the `fill`

aesthetic of dots, symbols, bars, boxes and violins.

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.

```
plot_dotbar_sd(data = data_cholesterol,
xcol = Treatment,
ycol = Cholesterol)
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
plot_dotbar_sd(data = data_1w_death,
xcol = Genotype, ycol = Death,
ColPal = "pale", ColSeq = FALSE, ColRev = TRUE)
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
#single colour along X
plot_dotbar_sd(data = data_1w_death,
xcol = Genotype, ycol = Death,
SingleColour = "light_orange")
#> Bin width defaults to 1/30 of the range of the data. Pick better value with
#> `binwidth`.
```