pbHeatmap | R Documentation |
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pbHeatmap( x, y, k = NULL, g = NULL, c = NULL, top_n = 20, fdr = 0.05, lfc = 1, sort_by = "p_adj.loc", decreasing = FALSE, assay = "logcounts", fun = mean, normalize = TRUE, col = viridis(10), row_anno = TRUE, col_anno = TRUE )
x |
a |
y |
a list of DS analysis results as returned by
|
k |
character vector; specifies which cluster ID(s) to retain.
Defaults to |
g |
character vector; specifies which genes to retain. Defaults to considering all genes. |
c |
character string; specifies which contrast/coefficient to retain.
Defaults to |
top_n |
single numeric; number of genes to retain per cluster. |
fdr, lfc |
single numeric; FDR and logFC cutoffs to filter results by.
The specified FDR threshold is applied to |
sort_by |
character string specifying
a numeric results table column to sort by;
|
decreasing |
logical; whether to sort
in decreasing order of |
assay |
character string; specifies which assay to use;
should be one of |
fun |
function to use as summary statistic, e.g., mean, median, sum (depending on the input assay). |
normalize |
logical; whether to apply a z-normalization to each row (gene) of the cluster-sample pseudobulk data. |
col |
character vector of colors or color mapping function
generated with |
row_anno, col_anno |
logical; whether to render annotations of cluster and group IDs, respectively. |
a HeatmapList-class
object.
Helena L Crowell
# compute pseudobulks & run DS analysis data(example_sce) pb <- aggregateData(example_sce) res <- pbDS(pb) # cluster-sample expression means pbHeatmap(example_sce, res) # include only a single cluster pbHeatmap(example_sce, res, k = "B cells") # plot specific gene across all clusters pbHeatmap(example_sce, res, g = "ISG20")
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