forked from Zaoqu-Liu/IRLS
-
Notifications
You must be signed in to change notification settings - Fork 0
/
All-signature-compare.R
249 lines (218 loc) · 10.1 KB
/
All-signature-compare.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
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
rm(list = ls())
library(dplyr)
library(data.table)
library(tidyr)
library(tibble)
library(survival)
library(survminer)
library(timeROC)
library(compareC)
library(ggsci)
load('all-signature.rda')
uni <- data.frame()
for (i in names(tmp2)) {
dd <- tmp2[[i]]
for(j in colnames(dd)[4:ncol(dd)]){
scox <- summary(coxph(Surv(OS.time,OS)~get(j),dd))
p <- compareC(dd$OS.time,dd$OS,dd$IRLS,dd[,j])$pval
uni <- rbind(uni,data.frame(ID=i,A=j,
HR=scox$conf.int[,1],
HR.95L=scox$conf.int[,3],
HR.95R=scox$conf.int[,4],
pvalue=scox$coefficients[,5],
cindex=scox$concordance[1]%>%as.numeric(),
cse=scox$concordance[2]%>%as.numeric(),
CP=p))
}
}
unique(uni$ID)
dd <- uni[uni$ID=='TCGA-CRC',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[1])+
ylab(NULL)+xlab(NULL)+
labs(title ="TCGA-CRC")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.89,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.5,0.7,0.9),limits = c(0.4,0.94))
# -------------------------------------------------------------------------
unique(uni$ID)
dd <- uni[uni$ID=='GSE17536',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[2])+
ylab(NULL)+xlab(NULL)+
labs(title ="GSE17536")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.71,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.5,0.6,0.7))
# -------------------------------------------------------------------------
unique(uni$ID)
dd <- uni[uni$ID=='GSE17537',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[3])+
ylab(NULL)+xlab(NULL)+
labs(title ="GSE17537")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.85,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.4,0.6,0.8),limits = c(0.38,0.88))
# -------------------------------------------------------------------------
unique(uni$ID)
dd <- uni[uni$ID=='GSE29621',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[4])+
ylab(NULL)+xlab(NULL)+
labs(title ="GSE29621")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.79,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.4,0.6,0.8),limits = c(0.36,0.82))
unique(uni$ID)
dd <- uni[uni$ID=='GSE38832',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[5])+
ylab(NULL)+xlab(NULL)+
labs(title ="GSE38832")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.78,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.4,0.6,0.8))
unique(uni$ID)
dd <- uni[uni$ID=='GSE39582',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[6])+
ylab(NULL)+xlab(NULL)+
labs(title ="GSE39582")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.69,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.5,0.6,0.7))
unique(uni$ID)
dd <- uni[uni$ID=='GSE72970',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[7])+
ylab(NULL)+xlab(NULL)+
labs(title ="GSE72970")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.69,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.5,0.6,0.7))
unique(uni$ID)
dd <- uni[uni$ID=='Meta-Cohort',]
dd$ll <- ifelse(dd$CP<0.0001,'****',ifelse(dd$CP<0.001,'***',ifelse(dd$CP<0.01,'**',ifelse(dd$CP<0.05,'*',''))))
rownames(dd) <- NULL
ggplot(dd,aes(cindex,reorder(A,cindex)))+
geom_errorbarh(aes(xmax=cindex+1.5*cse,xmin=cindex-1.5*cse),color="black",height=0,size=0.7)+
geom_point(size=4,shape=21,fill=pal_nejm()(10)[8])+
ylab(NULL)+xlab(NULL)+
labs(title ="Meta-Cohort")+
geom_vline(xintercept = 0.6,linetype='dashed',size=0.5,color='grey50')+
theme_bw(base_rect_size = 1)+
theme(panel.grid =element_blank(),
axis.text.y = element_text(size=12),
axis.text.x = element_text(size=12),
axis.title = element_text(size=13),
plot.title = element_text(hjust = 0.5,size=15),
legend.position = 'none',
strip.text = element_text(size=14))+
geom_text(aes(x=0.69,y=A,label=ll),color='black',size=3,vjust=0.76)+
scale_x_continuous(breaks = c(0.5,0.6,0.7))
# -------------------------------------------------------------------------
uni$x <- ifelse(uni$pvalue<0.05&uni$HR>1,'Risky',
ifelse(uni$pvalue<0.05&uni$HR<1,'Protective','P > 0.05'))
xx <- pivot_wider(uni[,c(1,2,10)],names_from = 'ID',values_from = 'x')
xx <- column_to_rownames(xx,'A')
library(ComplexHeatmap)
library(circlize)
ss <- read.csv('signature.csv')[,3:4]
ss <- distinct(ss,Author,.keep_all = T)
ss <- ss[ss$Author%in%rownames(xx),]
ss[107,] <- c('lncRNA','IRLS')
rownames(ss) <- ss$Author
ss <- ss[order(ss$Type,ss$Author),]
rownames(ss) <- NULL
xx <- xx[ss$Author,]
right = HeatmapAnnotation(Signature=ss$Type,
annotation_legend_param=list(labels_gp = gpar(fontsize = 12),border = T,
title_gp = gpar(fontsize = 12,fontface = "bold"),
ncol=1),
border = T,which = 'column',
col=list(Signature = c('lncRNA'=pal_npg(alpha = 0.8)(10)[3],'mRNA'=pal_nejm(alpha = 0.8)(8)[3])),
show_annotation_name = F,
annotation_name_gp = gpar(fontsize = 12))
Heatmap(t(xx),col = c('#F2F2F2',pal_npg()(2)[2],pal_npg()(2)[1]),name = 'Type',
rect_gp = gpar(col='grey70'),
top_annotation = right,
row_names_side = 'left',
heatmap_legend_param=list(labels_gp = gpar(fontsize = 12), border = T,
title_gp = gpar(fontsize = 12, fontface = "bold")))