`R/plot_3d_point_sd.R`

`plot_3d_point_sd.Rd`

One of 4 related functions for plotting 1-way ANOVA designs with a blocking factor.

`plot_3d_point_sd`

(mean & SD, SEM or CI95 error bars)`plot_3d_scatterbar`

(bar & SD, SEM or CI95 error bars)`plot_3d_scatterbox`

(box & whiskers)`plot_3d_scatterviolin`

(box & whiskers, violin)

```
plot_3d_point_sd(
data,
xcol,
ycol,
shapes,
facet,
ErrorType = "SD",
symsize = 3.5,
s_alpha = 1,
symshape = 22,
all_alpha = 0.3,
all_size = 2.5,
all_shape = 0,
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",
...
)
```

- data
a data table, e.g. data.frame or tibble.

- xcol
name of the column with the categorical factor to be plotted on X axis.

- ycol
name of the column with quantitative variable to plot on the Y axis.

- shapes
name of the column with the blocking factor or another categorical 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).

- symsize
size of symbols, default set to 3.

- s_alpha
fractional opacity of symbols, default set to 0.8 (i.e. 80% opacity). Set

`s_alpha = 0`

to not show scatter plot.- symshape
The mean is shown with symbol of the shape number 21 (default, filled circle). Pick a number between 0-25 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 0 (default, open square). 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"

- 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.- symthick
size (in 'pt' units) of outline of symbol lines (

`stroke`

), default =`fontsize`

/22.- ethick
thickness of 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`

palettes or base R to fill along X-axis aesthetic. Accepts any colour other than "black"; use`grey_lin11`

, which is almost black.- ...
any additional arguments to pass.

This function returns a `ggplot2`

object of class "gg" and "ggplot".

The blocking factor (or any other categorical variable) can be mapped to the `shapes`

argument (up to 25 levels allowed). Variables passed to `xcol`

and `shapes`

are internally converted to factors even if they are numeric or other type of variables.

In `plot_3d_point_sd`

and `plot_3d_scatterbar`

, the default error bar is SD (can be changed to SEM or CI95). In `plot_3d_point_sd`

, a large coloured symbol is plotted at the mean, all other data are shown as smaller symbols. Boxplot uses `geom_boxplot`

to depict median (thicker line), box (interquartile range (IQR)) and the whiskers (1.5*IQR).

Colours can be changed using `ColPal`

, `ColRev`

or `ColSeq`

arguments.
`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`

.

The resulting `ggplot2`

graph can take additional geometries or other layers.

```
#3d version for 1-way data with blocking
#use plot_point_sd when no a blocking factor is not used
plot_3d_point_sd(data = data_1w_death,
xcol = Genotype, ycol = Death,
shapes = Experiment)
```