plot-shc: plot shc object

Description Usage Arguments Details Value Author(s)


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


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



a shc object to plot produced by a call to shc


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)


a boolean specifyin whether rowlabels should be added as text along the bottom of the dendrogram (default = TRUE)


a double value corresponding to the hang parameter for the typical call to plot for an object of class hsigclust (default = -1)


a boolean specifying whether the FWER control procedure of Meinshausen et al. 2010 should be used. (default = TRUE)


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)


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)


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.