Description Usage Arguments Value Author(s) References Examples
Visualizes n x m association table as heatmap.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | 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')
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