View source: R/ReducedHeatmap.R
Compute Heatmap using dimensional reduction
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ReducedHeatmap(object, ...)
## Default S3 method:
ReducedHeatmap(object, features, dim_embedding,
cell_labels, enrich = 0, breaks = 100, slope = 50,
intercept = 0.05, dendrogram = "row", titleX = FALSE,
RowV = TRUE, show_legend = FALSE, hide_colorbar = FALSE,
fontsize_row = 7, margins = c(70, 50, NA, 0), ...)
## S3 method for class 'Seurat'
ReducedHeatmap(object, assay = NULL, slot = "data",
features = NULL, ident = NULL, reduction = "tsne", dimension = 1,
...)
## S3 method for class 'SingleCellExperiment'
ReducedHeatmap(object,
assay = "logcounts", features = NULL, ident = NULL,
reduction = "tsne", dimension = 1, ...)
|
object |
Object or expression matrix to visualize. Rownames should be gene names |
... |
Additional parameters to pass to heatmaply |
features |
Features to plot |
dim_embedding |
Cell embedding within the dimension of interest |
cell_labels |
Labels for each cell. While this is generally the cluster identity for a cell, it can be any discrete metadata variable |
enrich |
For every item in |
breaks |
Number of bins |
slope |
For better visualization, transform the values with a logistic function. This is the slope of that function. |
intercept |
For better visualization, transform the values with a logistic function. This is the intercept of that function. |
dendrogram |
See heatmaply help. Default: "row" |
titleX |
See heatmaply help. Default: FALSE. |
RowV |
See heatmaply help. Default: TRUE |
show_legend |
See heatmaply help. Default: FALSE |
hide_colorbar |
See heatmaply help. Default: FALSE |
fontsize_row |
See heatmaply help. Default: 7 |
margins |
See heatmaply help. Default: c(70, 50, NA, 0) |
assay |
Assay to use. Default: the object's current default assay. |
slot |
Slot to use. Default: "data" |
ident |
Object variable to use when determining cell_labels |
reduction |
Reduction to visualize. Default: 'umap' |
dimension |
The dimension to visualize. Default: 1 |
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