sc3_plot_markers: Plot expression of marker genes identified by 'SC3' as a...

Description Usage Arguments

Description

By default the genes with the area under the ROC curve (AUROC) > 0.85 and with the p-value < 0.01 are selected and the top 10 marker genes of each cluster are visualized in this heatmap.

Usage

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sc3_plot_markers.SingleCellExperiment(object, k, auroc, p.val, show_pdata)

## S4 method for signature 'SingleCellExperiment'
sc3_plot_markers(object, k, auroc = 0.85,
  p.val = 0.01, show_pdata = NULL)

Arguments

object

an object of 'SingleCellExperiment' class

k

number of clusters

auroc

area under the ROC curve

p.val

significance threshold used for the DE genes

show_pdata

a vector of colnames of the pData(object) table. Default is NULL. If not NULL will add pData annotations to the columns of the output matrix


hemberg-lab/SC3 documentation built on May 11, 2018, 4:32 p.m.