plot_iCN: Plot post-segmentation copy number profiles of integer values

In rujinwang/SCOPE: A normalization and copy number estimation method for single-cell DNA sequencing

Plot post-segmentation copy number profiles of integer values

Description

Show heatmap of inferred integer copy-number profiles by SCOPE with cells clustered by hierarchical clustering

Usage

plot_iCN(iCNmat, ref, Gini, annotation = NULL,
        plot.dendrogram = TRUE, show.names = FALSE, filename)

Arguments

iCNmat	inferred integer copy-number matrix by SCOPE, with each column being a cell and each row being a genomic bin
ref	GRanges object after quality control procedure
Gini	vector of Gini coefficients for each cell, with the same order as that of cells in columns of iCNmat
annotation	vector of annotation for each cell, with the same order as that of cells in columns of iCNmat. Default is NULL.
plot.dendrogram	logical, whether to plot the dendrogram. Default is TRUE.
show.names	logical, whether to show cell names by y axis. Default is FALSE.
filename	name of the output png file

Value

png file with integer copy-number profiles across single cells with specified annotations

Author(s)

Rujin Wang [e-mail]

Examples

Gini <- get_gini(Y_sim)
plot_iCN(iCNmat = iCN_sim,
        ref = ref_sim,
        Gini = Gini,
        filename = 'plot_iCN_demo')

rujinwang/SCOPE documentation built on Jan. 1, 2023, 5:40 a.m.