library(survival)
library(survminer)
## Loading required package: ggplot2
## Loading required package: ggpubr
##
## Attaching package: 'survminer'
## The following object is masked from 'package:survival':
##
## myeloma
setwd("~/Downloads")
a<-read.table("survival_times",header = TRUE)
aa<-data.frame(a)
b<-subset(a,aa$status==0)
c<-subset(a,aa$status==1)
summary(b)
## ID time status
## Length:249 Min. : -2 Min. :0
## Class :character 1st Qu.: 473 1st Qu.:0
## Mode :character Median : 1146 Median :0
## Mean : 1880 Mean :0
## 3rd Qu.: 2659 3rd Qu.:0
## Max. :11252 Max. :0
## NA's :9
summary(c)
## ID time status
## Length:220 Min. : 0.0 Min. :1
## Class :character 1st Qu.: 518.8 1st Qu.:1
## Mode :character Median : 1094.5 Median :1
## Mean : 1790.3 Mean :1
## 3rd Qu.: 2080.0 3rd Qu.:1
## Max. :10870.0 Max. :1
#compare
1880-1790.3
## [1] 89.7
setwd("~/Downloads")
ciber<-read.delim("CIBERSORTx_Job1_Adjusted2.txt")
#summary(ciber)
exa<-ciber[4,]
newciber<- ciber[,c(1,5)]
colnames(newciber)[1]<-'ID'
common<-merge(aa,newciber,by="ID")
design<-ifelse(common$T.cells.CD8>0.2,"CD8high","CD8low")
common<-cbind(common,design)
surv_object<-Surv(common$time,common$status)
survfit_object<-survfit(surv_object~common$design)
summary(survfit_object)
## Call: survfit(formula = surv_object ~ common$design)
##
## 9 observations deleted due to missingness
## common$design=CD8high
## time n.risk n.event survival std.err lower 95% CI upper 95% CI
## 216 154 1 0.994 0.00647 0.981 1.000
## 282 152 1 0.987 0.00915 0.969 1.000
## 315 148 1 0.980 0.01126 0.958 1.000
## 326 146 1 0.974 0.01303 0.948 0.999
## 424 136 1 0.966 0.01477 0.938 0.996
## 447 135 1 0.959 0.01631 0.928 0.992
## 468 133 1 0.952 0.01771 0.918 0.987
## 549 131 1 0.945 0.01901 0.908 0.983
## 601 126 1 0.937 0.02028 0.898 0.978
## 608 125 1 0.930 0.02146 0.889 0.973
## 650 122 1 0.922 0.02260 0.879 0.968
## 659 120 1 0.914 0.02368 0.869 0.962
## 710 117 1 0.907 0.02473 0.859 0.956
## 723 115 1 0.899 0.02574 0.850 0.951
## 821 111 1 0.891 0.02675 0.840 0.945
## 857 109 1 0.883 0.02773 0.830 0.939
## 877 108 2 0.866 0.02953 0.810 0.926
## 938 104 1 0.858 0.03039 0.800 0.920
## 955 103 1 0.850 0.03122 0.790 0.913
## 961 102 1 0.841 0.03200 0.781 0.906
## 1026 100 1 0.833 0.03277 0.771 0.900
## 1032 99 1 0.824 0.03350 0.761 0.893
## 1059 98 1 0.816 0.03420 0.752 0.886
## 1078 97 1 0.808 0.03487 0.742 0.879
## 1096 95 1 0.799 0.03552 0.732 0.872
## 1124 94 1 0.791 0.03615 0.723 0.865
## 1154 92 1 0.782 0.03676 0.713 0.857
## 1321 86 1 0.773 0.03744 0.703 0.850
## 1354 85 1 0.764 0.03809 0.693 0.842
## 1429 83 1 0.755 0.03872 0.682 0.834
## 1441 82 1 0.745 0.03933 0.672 0.827
## 1446 81 1 0.736 0.03991 0.662 0.819
## 1490 78 1 0.727 0.04050 0.652 0.811
## 1618 73 1 0.717 0.04115 0.640 0.802
## 1832 65 1 0.706 0.04197 0.628 0.793
## 1857 64 1 0.695 0.04273 0.616 0.784
## 1871 63 1 0.684 0.04345 0.604 0.774
## 1917 62 1 0.673 0.04413 0.591 0.765
## 1960 59 1 0.661 0.04483 0.579 0.755
## 1992 58 1 0.650 0.04548 0.567 0.745
## 2004 57 1 0.638 0.04609 0.554 0.735
## 2022 55 1 0.627 0.04669 0.542 0.725
## 2028 53 1 0.615 0.04729 0.529 0.715
## 2073 51 1 0.603 0.04787 0.516 0.704
## 2101 49 1 0.591 0.04845 0.503 0.694
## 2270 46 1 0.578 0.04907 0.489 0.682
## 2927 37 1 0.562 0.05017 0.472 0.670
## 3141 34 1 0.546 0.05135 0.454 0.656
## 3195 32 1 0.529 0.05250 0.435 0.642
## 3379 31 1 0.512 0.05350 0.417 0.628
## 3564 30 1 0.495 0.05437 0.399 0.613
## 4507 22 1 0.472 0.05635 0.374 0.596
## 4634 19 1 0.447 0.05861 0.346 0.578
## 4930 16 1 0.419 0.06125 0.315 0.558
## 6225 8 1 0.367 0.07263 0.249 0.541
## 6590 7 1 0.314 0.07893 0.192 0.514
##
## common$design=CD8low
## time n.risk n.event survival std.err lower 95% CI upper 95% CI
## 0 299 1 0.9967 0.00334 0.9901 1.000
## 79 290 1 0.9932 0.00478 0.9839 1.000
## 122 288 1 0.9898 0.00588 0.9783 1.000
## 151 286 1 0.9863 0.00680 0.9731 1.000
## 190 285 1 0.9828 0.00761 0.9681 0.998
## 196 284 1 0.9794 0.00833 0.9632 0.996
## 205 283 1 0.9759 0.00899 0.9585 0.994
## 237 278 1 0.9724 0.00962 0.9537 0.991
## 263 277 1 0.9689 0.01020 0.9491 0.989
## 264 276 1 0.9654 0.01075 0.9445 0.987
## 270 275 1 0.9619 0.01127 0.9400 0.984
## 274 274 1 0.9584 0.01177 0.9356 0.982
## 279 272 1 0.9549 0.01224 0.9312 0.979
## 284 271 1 0.9513 0.01269 0.9268 0.977
## 295 270 1 0.9478 0.01312 0.9224 0.974
## 308 268 1 0.9443 0.01354 0.9181 0.971
## 317 267 1 0.9407 0.01395 0.9138 0.968
## 319 266 1 0.9372 0.01434 0.9095 0.966
## 321 265 1 0.9337 0.01471 0.9053 0.963
## 326 262 1 0.9301 0.01508 0.9010 0.960
## 347 259 1 0.9265 0.01544 0.8967 0.957
## 352 258 1 0.9229 0.01580 0.8925 0.954
## 361 256 1 0.9193 0.01614 0.8882 0.951
## 368 255 2 0.9121 0.01680 0.8798 0.946
## 369 253 1 0.9085 0.01712 0.8756 0.943
## 383 250 1 0.9049 0.01743 0.8713 0.940
## 393 247 1 0.9012 0.01774 0.8671 0.937
## 394 246 1 0.8975 0.01804 0.8629 0.934
## 395 245 1 0.8939 0.01834 0.8586 0.931
## 396 244 1 0.8902 0.01862 0.8544 0.927
## 401 242 1 0.8865 0.01891 0.8502 0.924
## 412 238 1 0.8828 0.01919 0.8460 0.921
## 420 235 1 0.8790 0.01947 0.8417 0.918
## 422 234 1 0.8753 0.01975 0.8374 0.915
## 423 233 1 0.8715 0.02002 0.8332 0.912
## 425 232 1 0.8678 0.02028 0.8289 0.908
## 426 231 1 0.8640 0.02054 0.8247 0.905
## 430 230 1 0.8603 0.02079 0.8205 0.902
## 454 223 1 0.8564 0.02105 0.8161 0.899
## 467 221 1 0.8525 0.02131 0.8118 0.895
## 469 220 1 0.8487 0.02156 0.8074 0.892
## 470 219 1 0.8448 0.02181 0.8031 0.889
## 472 218 1 0.8409 0.02205 0.7988 0.885
## 504 212 1 0.8369 0.02230 0.7943 0.882
## 507 210 1 0.8330 0.02255 0.7899 0.878
## 516 209 1 0.8290 0.02279 0.7855 0.875
## 518 208 1 0.8250 0.02303 0.7811 0.871
## 519 207 1 0.8210 0.02326 0.7767 0.868
## 545 204 1 0.8170 0.02349 0.7722 0.864
## 561 201 1 0.8129 0.02372 0.7677 0.861
## 566 200 1 0.8088 0.02395 0.7632 0.857
## 613 195 1 0.8047 0.02418 0.7587 0.854
## 619 194 1 0.8005 0.02441 0.7541 0.850
## 620 193 1 0.7964 0.02463 0.7496 0.846
## 636 191 2 0.7881 0.02507 0.7404 0.839
## 673 186 1 0.7838 0.02529 0.7358 0.835
## 698 183 1 0.7795 0.02551 0.7311 0.831
## 721 181 1 0.7752 0.02573 0.7264 0.827
## 728 180 1 0.7709 0.02595 0.7217 0.823
## 730 179 1 0.7666 0.02616 0.7170 0.820
## 746 177 1 0.7623 0.02637 0.7123 0.816
## 787 171 1 0.7578 0.02659 0.7075 0.812
## 802 169 1 0.7533 0.02681 0.7026 0.808
## 808 166 1 0.7488 0.02703 0.6977 0.804
## 813 165 1 0.7443 0.02724 0.6927 0.800
## 818 164 1 0.7397 0.02745 0.6878 0.796
## 822 162 1 0.7352 0.02766 0.6829 0.791
## 824 161 1 0.7306 0.02786 0.6780 0.787
## 828 160 1 0.7260 0.02806 0.6731 0.783
## 832 158 1 0.7214 0.02825 0.6681 0.779
## 841 156 1 0.7168 0.02845 0.6632 0.775
## 843 155 1 0.7122 0.02864 0.6582 0.771
## 854 153 2 0.7029 0.02901 0.6483 0.762
## 874 151 1 0.6982 0.02919 0.6433 0.758
## 875 150 1 0.6936 0.02936 0.6383 0.754
## 884 149 1 0.6889 0.02953 0.6334 0.749
## 907 148 1 0.6843 0.02970 0.6285 0.745
## 988 147 1 0.6796 0.02986 0.6235 0.741
## 996 146 1 0.6749 0.03001 0.6186 0.736
## 1044 141 1 0.6702 0.03018 0.6135 0.732
## 1070 140 1 0.6654 0.03034 0.6085 0.728
## 1093 139 1 0.6606 0.03050 0.6034 0.723
## 1103 138 1 0.6558 0.03065 0.5984 0.719
## 1195 134 1 0.6509 0.03081 0.5932 0.714
## 1235 130 1 0.6459 0.03098 0.5879 0.710
## 1265 129 1 0.6409 0.03114 0.5827 0.705
## 1280 128 1 0.6359 0.03130 0.5774 0.700
## 1301 127 1 0.6309 0.03145 0.5722 0.696
## 1315 126 1 0.6259 0.03160 0.5669 0.691
## 1333 125 1 0.6209 0.03174 0.5617 0.686
## 1341 124 1 0.6159 0.03187 0.5565 0.682
## 1413 121 1 0.6108 0.03201 0.5511 0.677
## 1424 120 1 0.6057 0.03215 0.5458 0.672
## 1438 118 1 0.6005 0.03228 0.5405 0.667
## 1460 117 1 0.5954 0.03241 0.5352 0.662
## 1478 116 1 0.5903 0.03254 0.5298 0.658
## 1486 115 1 0.5851 0.03266 0.5245 0.653
## 1487 114 1 0.5800 0.03277 0.5192 0.648
## 1506 111 1 0.5748 0.03289 0.5138 0.643
## 1524 110 1 0.5696 0.03300 0.5084 0.638
## 1525 109 1 0.5643 0.03311 0.5030 0.633
## 1544 108 1 0.5591 0.03322 0.4977 0.628
## 1548 107 1 0.5539 0.03331 0.4923 0.623
## 1628 106 1 0.5487 0.03341 0.4869 0.618
## 1640 105 1 0.5434 0.03349 0.4816 0.613
## 1655 103 1 0.5382 0.03358 0.4762 0.608
## 1691 100 1 0.5328 0.03367 0.4707 0.603
## 1766 98 1 0.5273 0.03377 0.4651 0.598
## 1780 97 1 0.5219 0.03385 0.4596 0.593
## 1807 93 1 0.5163 0.03395 0.4539 0.587
## 1860 91 1 0.5106 0.03405 0.4481 0.582
## 1864 90 1 0.5049 0.03414 0.4423 0.576
## 1910 88 1 0.4992 0.03423 0.4364 0.571
## 1927 86 1 0.4934 0.03432 0.4305 0.565
## 2005 82 1 0.4874 0.03443 0.4244 0.560
## 2030 81 1 0.4814 0.03452 0.4182 0.554
## 2071 80 1 0.4754 0.03461 0.4121 0.548
## 2184 78 1 0.4693 0.03470 0.4059 0.542
## 2192 77 1 0.4632 0.03478 0.3998 0.537
## 2273 75 1 0.4570 0.03486 0.3935 0.531
## 2402 71 1 0.4506 0.03496 0.3870 0.525
## 2421 70 1 0.4441 0.03505 0.3805 0.518
## 2454 68 1 0.4376 0.03514 0.3739 0.512
## 2470 67 1 0.4311 0.03521 0.3673 0.506
## 2588 66 1 0.4245 0.03528 0.3607 0.500
## 2711 63 1 0.4178 0.03536 0.3539 0.493
## 2829 61 1 0.4109 0.03544 0.3470 0.487
## 2889 60 1 0.4041 0.03550 0.3402 0.480
## 2993 58 1 0.3971 0.03557 0.3332 0.473
## 3106 56 1 0.3900 0.03563 0.3261 0.467
## 3136 55 1 0.3829 0.03568 0.3190 0.460
## 3139 54 1 0.3758 0.03572 0.3120 0.453
## 3259 51 1 0.3685 0.03577 0.3046 0.446
## 3424 49 1 0.3610 0.03582 0.2972 0.438
## 3453 48 1 0.3534 0.03586 0.2897 0.431
## 3587 45 1 0.3456 0.03591 0.2819 0.424
## 3683 44 1 0.3377 0.03594 0.2741 0.416
## 3869 38 1 0.3288 0.03608 0.2652 0.408
## 3943 36 1 0.3197 0.03621 0.2561 0.399
## 4000 35 1 0.3106 0.03631 0.2470 0.391
## 4062 34 1 0.3014 0.03638 0.2379 0.382
## 4222 30 1 0.2914 0.03652 0.2279 0.373
## 4601 26 1 0.2802 0.03680 0.2166 0.362
## 4648 25 1 0.2690 0.03699 0.2054 0.352
## 5101 24 1 0.2578 0.03711 0.1944 0.342
## 5107 23 1 0.2466 0.03715 0.1835 0.331
## 5110 22 1 0.2354 0.03711 0.1728 0.321
## 5118 21 1 0.2241 0.03700 0.1622 0.310
## 5237 19 1 0.2123 0.03689 0.1511 0.298
## 5318 18 1 0.2006 0.03668 0.1401 0.287
## 5370 17 1 0.1888 0.03637 0.1294 0.275
## 6164 13 1 0.1742 0.03635 0.1158 0.262
## 6598 12 1 0.1597 0.03611 0.1025 0.249
## 6873 10 1 0.1437 0.03585 0.0882 0.234
## 6953 9 1 0.1278 0.03525 0.0744 0.219
## 7514 8 1 0.1118 0.03427 0.0613 0.204
## 8174 7 1 0.0958 0.03289 0.0489 0.188
## 9061 6 1 0.0799 0.03104 0.0373 0.171
## 10346 4 1 0.0599 0.02900 0.0232 0.155
## 10870 3 1 0.0399 0.02529 0.0115 0.138
ggsurvplot(survfit_object, data =common, risk.table = TRUE, pval = TRUE, conf.int = TRUE, legend.labs = c("CD8low", "CD8high"), xlab = "Time (days)", ylab = "Survival Probability", ggtheme = theme_bw())
