eccDNA clone analysis
The example or result data in the result folder can be downloaded here.
Merge the copy number amplification info of all samples
Calculate the number of fragments with copy number amplification in each cellCreate a data frame to record the copy number information of each eccDNA-related gene in each cell across all samples.
eccDNA_frame <- creat_eccDNA_frame(adapter.result.dir="eccDNAscope_example/result")
eccDNA_frame[1:5,1:3]## AK1_AGCTATGGTTTGACCA-1 AK1_CTGCTCAGTTTGTCTT-1 AK1_CCTGCTAAGTGGTGTG-1
## LINC02031 0 0 5
## LINC01854 6 0 0
## LINC02572 0 5 0
## HSPE1-MOB4 0 0 0
## SH3YL1 0 0 0Generate a Seurat object for eccDNA clone analysis
eccDNA_clone <- creat_eccDNA_clone_obj(eccDNA_frame=eccDNA_frame)
eccDNA_clone## An object of class Seurat
## 819 features across 1095 samples within 1 assay
## Active assay: RNA (819 features, 819 variable features)
## 3 layers present: counts, data, scale.data
## 2 dimensional reductions calculated: pca, umapeccDNA clone trajectory analysis
clone_result <- creat_eccDNA_clone_trajectory(eccDNA_clone_obj=eccDNA_clone,min.cor = 0.1)
clone_result$p
Extract all sub-paths from the eccDNA clone trajectory plot
all_sub_path <- extract_clone_branch(clone.result=clone_result$result)
all_sub_path## [1] "13->6->12->15->4->1->8->10" "13->6->12->15->4->9->5->10"
## [3] "13->12->15->4->1->8->10" "13->12->15->4->9->5->10"
## [5] "13->6->12->15->4->1->10" "13->6->12->15->4->9->10"
## [7] "13->6->12->15->4->5->10" "13->6->12->15->4->8->10"
## [9] "6->12->15->4->1->8->10" "6->12->15->4->9->5->10"
## [11] "13->6->12->4->1->8->10" "13->6->12->4->9->5->10"
## [13] "13->6->15->4->1->8->10" "13->6->15->4->9->5->10"
## [15] "13->12->15->4->1->10" "13->12->15->4->9->10"
## [17] "13->12->15->4->5->10" "13->12->15->4->8->10"
## [19] "13->6->12->15->4->10" "12->15->4->1->8->10"
## [21] "12->15->4->9->5->10" "6->12->15->4->1->10"
## [23] "6->12->15->4->9->10" "6->12->15->4->5->10"
## [25] "6->12->15->4->8->10" "13->12->4->1->8->10"
## [27] "13->12->4->9->5->10" "13->6->12->4->1->10"
## [29] "13->6->12->4->9->10" "13->6->12->4->5->10"
## [31] "13->6->12->4->8->10" "13->6->15->4->1->10"
## [33] "13->6->15->4->9->10" "13->6->15->4->5->10"
## [35] "13->6->15->4->8->10" "6->12->4->1->8->10"
## [37] "6->12->4->9->5->10" "6->15->4->1->8->10"
## [39] "6->15->4->9->5->10" "14->3->4->1->8->10"
## [41] "14->3->4->9->5->10" "14->2->4->1->8->10"
## [43] "14->2->4->9->5->10" "7->2->4->1->8->10"
## [45] "7->2->4->9->5->10" "13->12->15->4->10"
## [47] "13->6->12->15->10" "12->15->4->1->10"
## [49] "12->15->4->9->10" "12->15->4->5->10"
## [51] "12->15->4->8->10" "6->12->15->4->10"
## [53] "13->12->4->1->10" "13->12->4->9->10"
## [55] "13->12->4->5->10" "13->12->4->8->10"
## [57] "13->6->12->4->10" "13->6->15->4->10"
## [59] "12->4->1->8->10" "12->4->9->5->10"
## [61] "6->12->4->1->10" "6->12->4->9->10"
## [63] "6->12->4->5->10" "6->12->4->8->10"
## [65] "6->15->4->1->10" "6->15->4->9->10"
## [67] "6->15->4->5->10" "6->15->4->8->10"
## [69] "14->3->4->1->10" "14->3->4->9->10"
## [71] "14->3->4->5->10" "14->3->4->8->10"
## [73] "14->3->1->8->10" "14->4->1->8->10"
## [75] "14->4->9->5->10" "14->2->4->1->10"
## [77] "14->2->4->9->10" "14->2->4->5->10"
## [79] "14->2->4->8->10" "14->2->9->5->10"
## [81] "15->4->1->8->10" "15->4->9->5->10"
## [83] "3->4->1->8->10" "3->4->9->5->10"
## [85] "2->4->1->8->10" "2->4->9->5->10"
## [87] "7->2->4->1->10" "7->2->4->9->10"
## [89] "7->2->4->5->10" "7->2->4->8->10"
## [91] "7->2->9->5->10" "13->12->15->10"
## [93] "12->15->4->10" "6->12->15->10"
## [95] "13->12->4->10" "13->6->12->10"
## [97] "13->6->15->10" "12->4->1->10"
## [99] "12->4->9->10" "12->4->5->10"
## [101] "12->4->8->10" "6->12->4->10"
## [103] "6->15->4->10" "14->3->4->10"
## [105] "14->3->1->10" "14->3->5->10"
## [107] "14->3->8->10" "14->4->1->10"
## [109] "14->4->9->10" "14->4->5->10"
## [111] "14->4->8->10" "14->2->4->10"
## [113] "14->2->9->10" "14->2->5->10"
## [115] "14->9->5->10" "15->4->1->10"
## [117] "15->4->9->10" "15->4->5->10"
## [119] "15->4->8->10" "3->4->1->10"
## [121] "3->4->9->10" "3->4->5->10"
## [123] "3->4->8->10" "3->1->8->10"
## [125] "4->1->8->10" "4->9->5->10"
## [127] "2->4->1->10" "2->4->9->10"
## [129] "2->4->5->10" "2->4->8->10"
## [131] "2->9->5->10" "7->2->4->10"
## [133] "7->2->9->10" "7->2->5->10"
## [135] "12->15->10" "13->12->10"
## [137] "12->4->10" "6->12->10"
## [139] "6->15->10" "14->3->10"
## [141] "14->4->10" "14->2->10"
## [143] "14->9->10" "14->5->10"
## [145] "15->4->10" "3->4->10"
## [147] "3->1->10" "3->5->10"
## [149] "3->8->10" "4->1->10"
## [151] "4->9->10" "4->5->10"
## [153] "4->8->10" 2->4->10
## [155] "2->9->10" "2->5->10"
## [157] "7->2->10" "1->8->10"
## [159] "9->5->10" "12->10"
## [161] "14->10" "15->10"
## [163] "3->10" "4->10"
## [165] "2->10" "1->10"
## [167] "9->10" "5->10"
## [169] "8->10" "11->0"
## [171] "16->0"Plot a heatmap of genes with significant changes on the clone branches
p <- plot_clone_branch_features(clone_branch=c(2,4,10),
cluster_eccDNA=clone_result$cluster_eccDNA,
eccDNA_frame=eccDNA_frame,
eccDNA_clone=eccDNA_clone,
ncopy=10 )