`R/plot_point_sd.R`

`plot_point_sd.Rd`

This function takes a data table, categorical X and numeric Y variables, and plots a point showing the mean with SD error bars as default (SEM & CI95 are other options). The X variable is mapped to the `fill`

aesthetic of symbols.

```
plot_point_sd(
data,
xcol,
ycol,
facet,
ErrorType = "SD",
symsize = 3.5,
s_alpha = 1,
symshape = 21,
all_alpha = 0,
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",
...
)
```

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

- xcol
name of the column with a categorical X variable.

- ycol
name of the column with quantitative Y 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 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 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; i.e., not shown). 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"

- 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
thickness of symbol border, default set to

`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`

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`

stat_summary.

This function returns a `ggplot2`

object of class "gg" and "ggplot".

The function uses `stat_summary`

with `geom = "point"`

with `size = 3`

.
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)`

. `mean_se`

and `mean_cl_normal`

are used for SEM and CI95, respectively.

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.

You are instead encouraged to show all data using the following functions: `plot_scatterbar_sd`

, `plot_scatterbox`

, `plot_dotbox`

, `plot_dotbar_sd`

, `plot_scatterviolin`

or `plot_dotviolin`

.

```
#Basic usage
plot_point_sd(data = data_doubling_time,
xcol = Student, ycol = Doubling_time)
#show all data points
plot_point_sd(data = data_2w_Tdeath,
xcol = Genotype, ycol = PI,
facet = Time, all_alpha = 0.4)
```