Description Usage Arguments Value Examples
Plot a heatmap for counts.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | plotHeatmap(
se,
facet = as.formula("group~sample"),
transformFUN = log2,
pseudo = 1,
orderFUN = rowMeans,
orderBy = 1,
sampleOrder = NULL,
groupOrder = NULL,
fill_gradient = scale_fill_gradient(low = "blue", high = "red"),
boderColor = NA,
xaxis_breaks = NULL,
xaxis_label = NULL,
yaxis_breaks = NULL,
yaxis_label = NULL
)
|
se |
a SummarizedExperiment object from importCount. |
facet |
This will be passed to facet_grid:rows. It can be set to NULL. |
transformFUN |
The transform function of values. |
pseudo |
Pseudo value will be add to values before apply transformFUN. |
orderFUN |
function used to reorder Y axis of the heatmap |
orderBy |
the sample name or index used to order Y axis |
sampleOrder, groupOrder |
order of the samples(column) or groups(row). |
fill_gradient |
color fill gradient function. see scale_colour_gradient. |
boderColor |
The color of the heatmap cell border. |
xaxis_breaks, xaxis_label |
xaxis breaks and labels. see scale_x_continuous. |
yaxis_breaks, yaxis_label |
xaxis breaks and labels. see scale_y_discrete. |
ggplot object
1 2 3 | file <- system.file("extdata", "count.gz", package= "deepToolsDownstream")
se <- importCount(file)
plotHeatmap(se, yaxis_breaks="100033817", yaxis_label="geneA")
|
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