Draws a heatmap focusing on a principal component. Both cells and genes are sorted by their principal component scores. Allows for nice visualization of sources of heterogeneity in the dataset.
DimHeatmap(object, dims = 1, nfeatures = 30, cells = NULL,
reduction = "pca", disp.min = -2.5, disp.max = NULL,
balanced = TRUE, projected = FALSE, ncol = NULL, combine = TRUE,
fast = TRUE, raster = TRUE, slot = "scale.data", assays = NULL)PCHeatmap(object, ...)
Seurat object
Dimensions to plot
Number of genes to plot
A list of cells to plot. If numeric, just plots the top cells.
Which dimmensional reduction to use
Minimum display value (all values below are clipped)
Maximum display value (all values above are clipped); defaults to 2.5
if slot is 'scale.data', 6 otherwise
Plot an equal number of genes with both + and - scores.
Use the full projected dimensional reduction
Number of columns to plot
Combine plots into a single gg object; note that if TRUE; themeing will not work when plotting multiple dimensions
If true, use image to generate plots; faster than using ggplot2, but not customizable
If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE if you are encountering that issue (note that plots may take longer to produce/render).
Data slot to use, choose from 'raw.data', 'data', or 'scale.data'
A vector of assays to pull data from
Extra parameters passed to DimHeatmap
No return value by default. If using fast = FALSE, will return a ggplot object.
# NOT RUN {
DimHeatmap(object = pbmc_small)
# }
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