plot.Gene.Cor.Heatmap | R Documentation |
Generates a heatmap visualization of gene correlations based on expression data. Useful for identifying groups of genes that exhibit similar expression patterns across different conditions or cell types in a Seurat object.
## S3 method for class 'Gene.Cor.Heatmap'
plot(
genes,
assay.use = "RNA",
slot.use = c("data", "scale.data", "data.imputed")[1],
quantileX = 0.95,
min.g.cor = 0.3,
calc.COR = FALSE,
cutRows = NULL,
cutCols = cutRows,
obj = combined.obj,
...
)
genes |
Vector of gene symbols to include in the correlation analysis and heatmap. |
assay.use |
Assay from which to retrieve expression data within the Seurat object. Default: 'RNA'. |
slot.use |
Specifies which slot of the assay to use for expression data |
quantileX |
Quantile level for calculating expression thresholds. Default: |
min.g.cor |
Minimum absolute gene correlation value for inclusion in the heatmap. Default: |
calc.COR |
Logical flag to calculate correlation matrix if not found in |
cutRows |
Height at which to cut the dendrogram for rows, determining cluster formation. Default: |
cutCols |
Height at which to cut the dendrogram for columns, determining cluster formation.
Default: same as |
obj |
Seurat object containing the data. Default: |
... |
Additional parameters passed to the internally called functions. |
## Not run:
if (interactive()) {
plot.Gene.Cor.Heatmap(genes = c("Gene1", "Gene2", "Gene3"), obj = combined.obj)
}
## End(Not run)
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