correlation.heatmap: correlation.heatmap

Description Usage Arguments Value Author(s) References Examples

View source: R/correlation.heatmap.R

Description

Visualizes n x m correlation table as heatmap.

Usage

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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 microbiome-admin@googlegroups.com

References

See citation('microbiome')

Examples

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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.