Description Usage Arguments Value
Generate genotype plot (scatter plot) for each region and save in the plot directory.
1 2 3 4 5 6 7 8 9 10 | Lineage_plot(
Obj_filtered = NULL,
nSNP = 0,
clust_method = "ward.D2",
nclust = 5,
plot_conf = FALSE,
plot_path = NULL,
all_chr = FALSE,
maxcp = 6
)
|
Obj_filtered |
An Alleloscope object with a n cell by (m region * 2) genotype_values matrix and seg_table_filtered matrix. Every 2 columns in the genotype_values matrix are (rho_hat, theta_hat) of each region. |
nSNP |
An integer for the minimum number of SNPs across segments. Segments with the number of SNPs < nSNP are excluded. |
clust_method |
Method for clustering. Please refer to the "pheatmap" function. |
nclust |
An integer for the number of subclones gapped in the plot. |
plot_conf |
Logical (TRUE/FALSE). Whether or not to plot the confidence scores under the lineage tree. |
plot_path |
The path for saving the plot. |
all_chr |
Logical (TRUE/FALSE). Whether or not the analysis is at the whole-genome level. |
maxcp |
Integer. Setting the maximum number of copies for the analysis. |
Plot the lineage tree constructed using cell-level genotypes across all regions and return a vector indicating the cluster identity (of the nclust clusters) of each cell.
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