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

View source: R/plot_iCN.R

plot_iCNR Documentation

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 rujin@email.unc.edu

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.