pbHeatmap | R Documentation |
...
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")
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.