Data input for pandemonium

Inputs

To use the app, the user needs to provide an array of observations of variables. Variables are sorted into the clustering space (space1) and the linked space (space2) once loaded into the app in the data screen.

Alternatively they can be passed to as two separate arrays with the clustering variables in df = space1 and the linked variables in space2 = space2. This will select them in space 1 and 2 in the data screen when loading the app. This can be done like this:

newPandemonium(df = Bikes$space1, space2 = Bikes$space2)

Once data has been selected press load data button to begin analysis using the app. See “Data Analysis” for more information in this.

Optional inputs

A complete input for pandemonium includes optional data and function inputs. The all inputs are shown in the following call.

pandemonium(df, cov = NULL, is.inv = FALSE, exp = NULL, space2 = NULL, space2.cov = NULL, 
            space2.exp = NULL, group = NULL, label = NULL, user_dist = NULL, 
            dimReduction = list(tSNE = tSNE, umap = umap), getCoords = list(normal = normCoords), getScore = NULL)

Data Inputs

Input	Type	Applies to	Default	Purpose
label	vector, length = n	points	row index	Shown in tours/dim. reduction hover text
group	vector / data.frame	points	none	Define user-specified groups; categorical or numeric
cov,space2.cov*	matrix	group/space	computed via stats::cov	Used in getScores, getCoords, anomaly tour
exp,space2.exp	data frame with column value length of number of variables in space	variables	mean vector	Reference point in space used in getCoords
user_dists	matrix	space1	ignored	Advanced: overrides getDists output

* cov can also be the inverse covariance matrix by setting is.Inv=TRUE

Function inputs

Input	Type	Use
getCoords	named list of coordinate functions	computes coordinates for distance calculations
getScores	Function that rurns a named list	computes scores and/or bins for use in plotting

See vignette("getScores") and vignette("getCoords") for more information on these inputs.