docs/functions/plot.circos.md

In jgygi/SPEAR: SPEAR - Sparse Supervised Bayesian Factor Model for Multi-omic Analyses

plot.circos

Plot a circos plot (chord diagram) for a correlation matrix supplied. Rows and columns need to be found in colnames(SPEARobj$data$train$X).

Description

Plot a circos plot (chord diagram) for a correlation matrix supplied. Rows and columns need to be found in colnames(SPEARobj$data$train$X).

Usage

list(list("plot"), list("circos"))(
  correlation.matrix = NULL,
  correlation.cutoff = 0.5,
  allow.same.dataset = FALSE,
  sign = "both",
  highlight.feature = NULL,
  highlight.color = "black",
  highlight.emphasis = 2.5
)

Arguments

Argument |Description ------------- |---------------- correlation.matrix | Which factors to return features for? Accepts integers (i.e. factors = c(1,2,4) or factors = 1) Defaults to NULL (all). correlation.cutoff | What is the correlation cutoff to be included in the plot? Defaults to 0.5 allow.same.dataset | Should connections within the same dataset be plotted? Defaults to FALSE sign | Which direction of correlations to show? Can be "both" (default), "pos" (positive), or "negative" (negative). highlight.feature | Should one feature be highlighted in the plot? Can be a string (the feature name). Feature must be found in the final plot to be highlighted. Defaults to NULL (no highlighting) highlight.color | What color to highlight the highlight.feature connections? Defaults to "black" highlight.emphasis | How much should the highlight.feature connections be emphasized? 1 will put the same size as other connections. Defaults to 2.5

jgygi/SPEAR documentation built on July 5, 2023, 5:35 p.m.