fx.get_circle_df: Make a data.frame for encircling points in a reduced...
In evanbiederstedt/sandbox: The functions

Description Usage Arguments Details Value See Also

For the encircling, we will use the values of X and Y to determine the coordinates for the circle that will either capture all values, or those within the quantile defined by which_quant. Multiple circles may be drawn based on groups provided via separate_by.

1 2	fx.get_circle_df(in.df, X = "x_axs", Y = "y_axs", separate_by = NULL, keep_quant = 1)

`in.df`	data.frame that is used for making the original plot.
`X`	name (or integer index) of the column of in.df that contains the values to be used for determining the x axis coordinates (default: "x_axs").
`Y`	name (or integer index) of the column that contains the values to be used for determining the y axis coordinates (default: "y_axs".,
`separate_by`	factor that will be used to split the values of X and Y into distinct groups (e.g., by "condition"); if NULL (default), `which_quant`
`keep_quant`	a number between 0.5 and 1 to define the max. quantile for any value of `X` or `Y` that will be kept for defining the circle coordinates. The default is to capture all points that belong to one instance of `separate_by`, i.e. `keep_quant= 1`. It might be useful to set it to less than 1 (e.g., 0.99) if you don't want the circle to be blown up by individual outliers. 0.99 would ensure that only those points between the 99th percentile and the 0.01st percentile (1 - 0.99) would be kept.

Sometimes, it is useful to remove outlier coordinates before drawing the circles. If keep_quant= 1, the output will be exactly the content of in.df. keep_quant should be a number between 1 and 0.5, usually you will want to use something between 0.95 and 1.

Integer indeces for X and Y must be given in proper integer notation (e.g., 1L) so that is.integer(X) passes.

data.table, most likely a subset of the in.df, depending on the setting of which_quant. This data.table can be used with ggalt::geom_encircle.

plot_reduced_dim.df, scABC2::generate.DimRedPlot

evanbiederstedt/sandbox documentation built on May 26, 2019, 12:31 p.m.