ggparci: Parallel Coordinates Plot with Groups medians and their...

In HBPMedical/ggparci: Parallel Coordinates Plot with Groups medians and their Confidence Intervals

Description

The function plots parallel coordinates (gg)plot, in which each line connects the variables medians for each group. Confidence "bands" for the medians are added to each line. This allows the assessment of groups (clusters) separations. The variables are normalized to [0,1] scale prior to plotting.

Usage

ggparci(data, columns = 1:ncol(data), groups_column, conf_level = 0.95,
  method = c("normalize", "percentize", "none"), title = "",
  groups_in_facets = FALSE, flip_coords = FALSE,
  include_obs_lines = FALSE, alpha_obs_lines = 0.1, alpha_ci_bands = 0.5,
  ...)

Arguments

data	a data.frame. includes the grouping variable
columns	variables to include in the plot, as character vector with columns names or as integer vector with positions. the group variable is ignored, if specified.
groups_column	grouping variable name (quoted)
conf_level	confidence level for the bands, Default: 0.95
method	which normalization method to apply. See normalize (default) and percentize.
title	Plot title, Default: ”
groups_in_facets	logical. plot each group in a separate plot/facet? Default: FALSE
flip_coords	logical. make the coordinates horizontal? Default: FALSE
include_obs_lines	logical. add lines for the rows? Default: FALSE
alpha_obs_lines	transparency factor for the lines, Default: 0.1
alpha_ci_bands	transparency factor for the confidence bands, Default: 0.5
...	additional arguments to the plot

Value

a ggplot object

Examples

## Not run: 

ggparci(iris, groups_column = "Species", method = "none")
ggparci(iris, groups_column = "Species", method = "normalize")
ggparci(iris, groups_column = "Species", method = "percentize")

#select only some of the variables
# plot a line for each observation
# and dont plot the CIs
ggparci(iris,columns = 1:3, groups_column = "Species", include_obs_lines = T, alpha_ci_bands = 0)

# display each group in a different facet
ggparci(iris, groups_column = "Species", groups_in_facets = T)

# flip the plot
ggparci(iris, groups_column = "Species", flip_coords = T)


## End(Not run)

HBPMedical/ggparci documentation built on May 28, 2019, 12:40 p.m.