jaccard_heatmap: Create a heatmap of the Jaccard similarity index (JSI)...
| jaccard_heatmap | R Documentation |
Create a heatmap of the Jaccard similarity index (JSI) between samples of an experiment
Description
This function creates a JSI heatmap between all samples in the expression matrix using the specified number of most abundant genes as input. Metadata columns are used as annotations.
Usage
jaccard_heatmap( expression.matrix, metadata, top.annotation.ids = NULL, n.abundant = NULL, show.values = TRUE, show.row.column.names = TRUE )
Arguments
expression.matrix |
the expression matrix; rows correspond to genes and
columns correspond to samples; usually preprocessed by
|
metadata |
a data frame containing metadata for the samples contained
in the expression.matrix; must contain at minimum two columns:
the first column must contain the column names of the expression.matrix,
while the last column is assumed to contain the experimental conditions
that will be tested for differential expression; a list (of the same
length as modality) can be provided if #' |
top.annotation.ids |
a vector of column indices denoting which columns of the metadata should become heatmap annotations |
n.abundant |
number of most abundant genes to use for the JSI calculation |
show.values |
whether to show the JSI values within the heatmap squares |
show.row.column.names |
whether to show the row and column names below the heatmap; default is TRUE |
Value
The JSI heatmap as detailed in the ComplexHeatmap package.
Examples
expression.matrix.preproc <- as.matrix(read.csv(
system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"),
row.names = 1
))[1:500,]
metadata <- data.frame(
srr = colnames(expression.matrix.preproc),
timepoint = rep(c("0h", "12h", "36h"), each = 2)
)
print(jaccard_heatmap(expression.matrix.preproc, metadata, n.abundant = 100))
