-
Notifications
You must be signed in to change notification settings - Fork 1
/
Copy pathdeeann_cellchat.R
95 lines (72 loc) · 4.01 KB
/
deeann_cellchat.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
head(deeann)
deeann_control <- subset(deeann, subset = orig.ident == 'control')
deeann_treated <- subset(deeann, subset = orig.ident == 'treated')
cellchat <- createCellChat(object = deeann_control, group.by = "cell type")
CellChatDB <- CellChatDB.human
CellChatDB.use <- CellChatDB
cellchat@DB <- CellChatDB.use
cellchat <- subsetData(cellchat)
cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)
cellchat <- projectData(cellchat, PPI.human)
cellchat <- computeCommunProb(cellchat, type = "truncatedMean", trim = 0.2, raw.use = FALSE, population.size = TRUE)
cellchat <- filterCommunication(cellchat, min.cells = 3)
cellchat <- computeCommunProbPathway(cellchat)
cellchat <- aggregateNet(cellchat)
cellchat <- netAnalysis_computeCentrality(cellchat, slot.name = "netP")
cellchat_control <- cellchat
cellchat <- createCellChat(object = deeann_treated, group.by = "cell type")
CellChatDB <- CellChatDB.human
CellChatDB.use <- CellChatDB
cellchat@DB <- CellChatDB.use
cellchat <- subsetData(cellchat)
cellchat <- identifyOverExpressedGenes(cellchat)
cellchat <- identifyOverExpressedInteractions(cellchat)
cellchat <- projectData(cellchat, PPI.human)
cellchat <- computeCommunProb(cellchat, type = "truncatedMean", trim = 0.2, raw.use = FALSE, population.size = TRUE)
cellchat <- filterCommunication(cellchat, min.cells = 3)
cellchat <- computeCommunProbPathway(cellchat)
cellchat <- aggregateNet(cellchat)
cellchat <- netAnalysis_computeCentrality(cellchat, slot.name = "netP")
cellchat_treated <- cellchat
ht1 <- netAnalysis_signalingRole_heatmap(cellchat_control, pattern = "outgoing")
ht2 <- netAnalysis_signalingRole_heatmap(cellchat_control, pattern = "incoming")
ht1 + ht2
ht1 <- netAnalysis_signalingRole_heatmap(cellchat_treated, pattern = "outgoing")
ht2 <- netAnalysis_signalingRole_heatmap(cellchat_treated, pattern = "incoming")
ht1 + ht2
strwidth <- function(x) {0.5}
netVisual_chord_cell(cellchat_control, signaling = 'THBS')
netVisual_chord_cell(cellchat_treated, signaling = 'THBS')
netVisual_chord_cell(cellchat_control, signaling = 'CNTN')
netVisual_chord_cell(cellchat_treated, signaling = 'CNTN')
netVisual_chord_cell(cellchat_control, signaling = 'PERIOSTIN')
netVisual_chord_cell(cellchat_treated, signaling = 'PERIOSTIN')
netVisual_chord_cell(cellchat_control, signaling = 'NT')
netVisual_chord_cell(cellchat_treated, signaling = 'NT')
netVisual_chord_cell(cellchat_control, signaling = 'CD86')
netVisual_chord_cell(cellchat_treated, signaling = 'CD86')
netVisual_chord_cell(cellchat_control, signaling = 'NRG')
netVisual_chord_cell(cellchat_treated, signaling = 'NRG')
netVisual_chord_cell(cellchat_control, signaling = 'RELN')
netVisual_chord_cell(cellchat_treated, signaling = 'RELN')
netVisual_chord_cell(cellchat_control, signaling = 'NECTIN')
netVisual_chord_cell(cellchat_treated, signaling = 'NECTIN')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'CXCL')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'CXCL')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'CD23')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'CD23')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'CD6')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'CD6')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'ALCAM')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'ALCAM')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'KIT')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'KIT')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'LIFR')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'LIFR')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'LIGHT')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'LIGHT')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'CDH')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'CDH')
netVisual_chord_cell(cellchat_control_no_endo, signaling = 'IL6')
netVisual_chord_cell(cellchat_treated_no_endo, signaling = 'IL6')