-
Notifications
You must be signed in to change notification settings - Fork 0
/
plotly_2.R
140 lines (131 loc) · 3.85 KB
/
plotly_2.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
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
#️ パッケージインストール（一度やればよい）
install.packages("devtools")
library("devtools")
devtools::install_github("ropensci/plotly")
# パッケージ読み込み
# Learn about API authentication here: https://plot.ly/r/getting-started
# に自分のユーザー名とAPIキーが表示される
library(plotly)
# データ読み込み
load("pca2.Rdata")
# 名前がついたベクトルはplotlyでは受け付けない
rownames(pca2$rotation) <- NULL
makePlotly2 <- function(user, apikey){
set_credentials_file(user, apikey)
py <- plotly()
BCell <- list(
x = pca2$rotation[which(Label2$group_name == "B cell"), 1],
y = pca2$rotation[which(Label2$group_name == "B cell"), 2],
z = pca2$rotation[which(Label2$group_name == "B cell"), 3],
mode = "markers+text",
name = "B Cell",
text = Label2$Well[which(Label2$group_name == "B cell")],
textfont = list(
color = "rgb(102, 102, 102)",
size = 7),
marker = list(
size = 12,
line = list(
color = "rgba(217, 217, 217, 0.14)",
width = 0.5
),
opacity = 0.8
),
type = "scatter3d"
)
NKTCell <- list(
x = pca2$rotation[which(Label2$group_name == "NK_cell"), 1],
y = pca2$rotation[which(Label2$group_name == "NK_cell"), 2],
z = pca2$rotation[which(Label2$group_name == "NK_cell"), 3],
mode = "markers+text",
name = "NKT Cell",
text = Label2$Well[which(Label2$group_name == "NK_cell")],
textfont = list(
color = "rgb(102, 102, 102)",
size = 7),
marker = list(
size = 12,
line = list(
color = "rgba(50, 217, 217, 0.14)",
width = 0.5
),
opacity = 0.8
),
type = "scatter3d"
)
DC <- list(
x = pca2$rotation[which(Label2$group_name == "CD8+pDC"), 1],
y = pca2$rotation[which(Label2$group_name == "CD8+pDC"), 2],
z = pca2$rotation[which(Label2$group_name == "CD8+pDC"), 3],
mode = "markers+text",
name = "DC",
text = Label2$Well[which(Label2$group_name == "CD8+pDC")],
textfont = list(
color = "rgb(102, 102, 102)",
size = 7),
marker = list(
size = 12,
line = list(
color = "rgba(217, 50, 217, 0.14)",
width = 0.5
),
opacity = 0.8
),
type = "scatter3d"
)
Monocyte <- list(
x = pca2$rotation[which(Label2$group_name == "monocyte_or_neutrophil"), 1],
y = pca2$rotation[which(Label2$group_name == "monocyte_or_neutrophil"), 2],
z = pca2$rotation[which(Label2$group_name == "monocyte_or_neutrophil"), 3],
mode = "markers+text",
name = "Monocyte",
text = Label2$Well[which(Label2$group_name == "monocyte_or_neutrophil")],
textfont = list(
color = "rgb(102, 102, 102)",
size = 7),
marker = list(
size = 12,
line = list(
color = "rgba(217, 217, 50, 0.14)",
width = 0.5
),
opacity = 0.8
),
type = "scatter3d"
)
data <- list(BCell, NKTCell, DC, Monocyte)
layout <- list(
scene = list(
xaxis = list(
title = "1st Component",
gridcolor = "rgb(255, 255, 255)",
showbackground = TRUE,
spikecolor = "rgb(102, 102, 102)",
backgroundcolor = "rgb(210, 210, 210)"
),
yaxis = list(
title = "2nd Component",
gridcolor = "rgb(255, 255, 255)",
showbackground = TRUE,
spikecolor = "rgb(102, 102, 102)",
backgroundcolor = "rgb(210, 210, 210)"
),
zaxis = list(
title = "3rd Component",
gridcolor = "rgb(255, 255, 255)",
showbackground = TRUE,
spikecolor = "rgb(102, 102, 102)",
backgroundcolor = "rgb(210, 210, 210)"
)
),
margin = list(
l = 0,
r = 0,
b = 0,
t = 0
)
)
response <- py$plotly(data, kwargs=list(layout=layout, filename="MARS-Seq", fileopt="overwrite"))
url <- response$url
url
}