outcome2factor: Convert numeric ternary outcomes into a factor

In ggpmisc: Miscellaneous Extensions to 'ggplot2'

Convert numeric ternary outcomes into a factor

Description

Convert numeric ternary outcomes into a factor

Usage

outcome2factor(x, n.levels = 3L)

threshold2factor(x, n.levels = 3L, threshold = 0)

Arguments

x	a numeric vector of -1, 0, and +1 values, indicating down-regulation, uncertain response or up-regulation, or a numeric vector that can be converted into such values using a pair of thresholds.
n.levels	numeric Number of levels to create, either 3 or 2.
threshold	numeric vector Range enclosing the values to be considered uncertain.

Details

These functions convert the numerically encoded values into a factor with the three levels "down", "uncertain" and "up", or into a factor with two levels de and uncertain as expected by default by scales scale_colour_outcome, scale_fill_outcome and scale_shape_outcome. When n.levels = 2 both -1 and +1 are merged to the same level of the factor with label "de".

Note

These are convenience functions that only save some typing. The same result can be achieved by a direct call to factor and comparisons. These functions aim at making it easier to draw volcano and quadrant plots.

See Also

Other Functions for quadrant and volcano plots: FC_format(), scale_colour_outcome(), scale_shape_outcome(), scale_y_Pvalue(), xy_outcomes2factor()

Other scales for omics data: scale_colour_logFC(), scale_shape_outcome(), scale_x_logFC(), xy_outcomes2factor()

Examples

outcome2factor(c(-1, 1, 0, 1))
outcome2factor(c(-1, 1, 0, 1), n.levels = 2L)

threshold2factor(c(-0.1, -2, 0, +5))
threshold2factor(c(-0.1, -2, 0, +5), n.levels = 2L)
threshold2factor(c(-0.1, -2, 0, +5), threshold = c(-1, 1))

ggpmisc documentation built on Nov. 16, 2023, 5:10 p.m.