plot-shc: plot shc object
In pkimes/sigclust2: sigclust2: Statistical Significance of Clustering

Description Usage Arguments Details Value Author(s)

Visualize the results of SHC analysis as an annotated dendrogram with significant branches highlighted

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## S3 method for class 'shc'
plot(x, groups = NULL, use_labs = TRUE, hang = -1,
  fwer = TRUE, alpha = NULL, ci_idx = NULL, ci_emp = NULL, ...)

`x`	a `shc` object to plot produced by a call to `shc`
`groups`	a vector specifying group labels for the clustered objects. The vector should be in the same order as the rows of the original data matrix. If specified, color blocks will be placed along the bottom of the dendrogram. Useful when the samples have a priori known groupi behavior. (default = `NULL`)
`use_labs`	a boolean specifyin whether rowlabels should be added as text along the bottom of the dendrogram (default = `TRUE`)
`hang`	a double value corresponding to the `hang` parameter for the typical call to `plot` for an object of class `hsigclust` (default = -1)
`fwer`	a boolean specifying whether the FWER control procedure of Meinshausen et al. 2010 should be used. (default = `TRUE`)
`alpha`	a double between 0 and 1 specifying the significance cutoff. If `fwer` is TRUE, the FWER of the entire dendrogram is controlled at `alpha`, else, each branch is tested at `alpha`. Only has effect if `alpha(shc)` = 1. (default = 0.05 or `alpha` used for `x` if original `shc` called with `alpha` < 1)
`ci_idx`	a numeric value between 1 and `length(ci)` specifiying which CI to use for the FWER stopping rule. This only has an effect if `alpha` < 1. (default = 1 or `ci_idx` used for `x` if original `shc` called with `alpha` < 1 or `fwer` = TRUE)
`ci_emp`	a logical value specifying whether to use the empirical p-value from the CI based on `ci_idx` for the FWER stopping rule. As with `ci_idx` this only has an effect if `alpha` < 1. (default = FALSE or `ci_emp` used for `x` if original `shc` called with `alpha` < 1 or `fwer` = TRUE)
`...`	other parameters to be used by the function

This function makes use of dendrogram plotting functions made available through the ggdendro package which provides a ggplot2-like grammer for working with dendrograms.

ggplot object containing a dendrogram annotated by the results of the corresponding shc analysis

Patrick Kimes

pkimes/sigclust2 documentation built on May 25, 2019, 8:20 a.m.