correlation.heatmap: correlation.heatmap

In microbiome/microbiomeold: Tools for microbiome analysis

Description

Visualizes n x m correlation table as heatmap.

Usage

correlation.heatmap(df, Xvar, Yvar, fill, star = "p.adj",
  p.adj.threshold = 1, correlation.threshold = 0, step = 0.2,
  colours = c("darkblue", "blue", "white", "red", "darkred"), limits = NULL,
  legend.text = "", order.rows = TRUE, order.cols = TRUE,
  text.size = 10, filter.significant = TRUE, star.size = NULL)

Arguments

df	Data frame. Each row corresponds to a pair of correlated variables. The columns give variable names, correlations and significance estimates.
Xvar	X axis variable column name. For instance 'X'.
Yvar	Y axis variable column name. For instance 'Y'.
fill	Column to be used for heatmap coloring. For instance 'correlation'.
star	Column to be used for cell highlighting. For instance 'p.adj'.
p.adj.threshold	Significance threshold for the stars.
correlation.threshold	Include only elements that have absolute correlation higher than this value
step	color interval
colours	heatmap colours
limits	colour scale limits
legend.text	legend text
order.rows	Order rows to enhance visualization interpretability
order.cols	Order columns to enhance visualization interpretability
text.size	Adjust text size
filter.significant	Keep only the elements with at least one significant entry
star.size	NULL Determine size of the highlight symbols

Value

ggplot2 object

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

data(peerj32)
  d1 <- peerj32$lipids[, 1:10]
  d2 <- peerj32$microbes[, 1:10]
  cc <- cross.correlate(d1, d2)
  p <- correlation.heatmap(cc, 'X1', 'X2', 'Correlation')

microbiome/microbiomeold documentation built on May 22, 2019, 9:57 p.m.