heat {microbiome} | R Documentation |
Visualizes n x m association table as heatmap.
heat(df, Xvar = names(df)[[1]], Yvar = names(df)[[2]], fill = names(df)[[3]], star = NULL, p.adj.threshold = 1, association.threshold = 0, step = 0.2, colours = c("darkblue", "blue", "white", "red", "darkred"), limits = NULL, legend.text = "", order.rows = TRUE, order.cols = TRUE, filter.significant = TRUE, star.size = NULL, plot.values = FALSE)
df |
Data frame. Each row corresponds to a pair of associated variables. The columns give variable names, association scores 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 'association'. |
star |
Column to be used for cell highlighting. For instance 'p.adj'. |
p.adj.threshold |
Significance threshold for the stars. |
association.threshold |
Include only elements that have absolute association 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. If this is logical, then hclust is applied. If this is a vector then the rows are ordered using this index. |
order.cols |
Order columns to enhance visualization interpretability. If this is logical, then hclust is applied. If this is a vector then the rows are ordered using this index. |
filter.significant |
Keep only the elements with at least one significant entry |
star.size |
NULL Determine size of the highlight symbols |
plot.values |
Show values as text |
ggplot2 object
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation('microbiome')
data(peerj32) d1 <- peerj32$lipids[, 1:10] d2 <- peerj32$microbes[, 1:10] cc <- associate(d1, d2, method='pearson') p <- heat(cc, 'X1', 'X2', 'Correlation', star='p.adj')