小提琴图代码
1. 单个基因表达_临床特征分组
输入数据：
id Stage SEMA3A TCGA-F1-6177-01A Stage I 0.2202665 TCGA-IN-A6RI-01A Stage I 0.1181326 TCGA-VQ-A8PX-01A Stage I 0.391461954 TCGA-HU-8610-01A Stage I 0.9027969 TCGA-IN-A6RJ-01A Stage I 0.226128517 TCGA-F1-6875-01A Stage I 2.588222513 TCGA-BR-8486-01A Stage I 0.773641359 TCGA-HU-A4G9-01A Stage I 0.1595753 TCGA-CG-4443-01A Stage I 0.142903267 TCGA-IN-A6RO-01A Stage I 0.6163783 TCGA-IN-A6RS-01A Stage I 0.3461303 TCGA-CG-5726-01A Stage I 0.1253805 TCGA-IN-AB1V-01A Stage I 0.452058009 TCGA-HU-8244-01A Stage I 0.370961995 TCGA-HF-7134-01A Stage I 0.4566849 TCGA-HU-A4GH-01A Stage I 0.470165863 TCGA-CG-5720-01A Stage I 0.4694241 TCGA-KB-A93G-01A Stage I 0.527477971 TCGA-VQ-A8DV-01A Stage I 0.942445321 TCGA-B7-5818-01A Stage I 0.242827964 TCGA-FP-8209-01A Stage I 0.889732937 TCGA-CG-4466-01A Stage I 0.597073098 TCGA-CG-4477-01A Stage I 0.93565655 TCGA-HU-A4H5-01A Stage I 0.5803231 TCGA-D7-A6F2-01A Stage I 0.739902864 TCGA-BR-4267-01A Stage I 0.419723925 TCGA-HU-A4H8-01A Stage I 0.2352173 TCGA-FP-7735-01A Stage I 0.6413326 TCGA-BR-8679-01A Stage I 1.286488303 TCGA-CG-5725-01A Stage I 0.4610466 TCGA-RD-A7C1-01A Stage I 0.793228475 TCGA-BR-8368-01A Stage I 0.241820974 TCGA-CG-4436-01A Stage I 1.213049 TCGA-CG-4442-01A Stage I 1.55303475 TCGA-SW-A7EA-01A Stage I 0.120073 TCGA-D7-A6F0-01A Stage I 0.2823409 TCGA-HJ-7597-01A Stage I 0.66829068 TCGA-CG-4304-01A Stage I 1.043310125 TCGA-D7-6528-01A Stage I 0.259943978 TCGA-D7-8578-01A Stage I 1.868535316 TCGA-VQ-A92D-01A Stage I 0.30548 TCGA-RD-A8N2-01A Stage I 3.535827105 TCGA-ZA-A8F6-01A Stage I 2.019519 TCGA-RD-A7BW-01A Stage I 2.36891042 TCGA-BR-7707-01A Stage I 0.2068636 TCGA-KB-A6F7-01A Stage I 0.766425706 TCGA-D7-6522-01A Stage I 0.798488815 TCGA-3M-AB46-01A Stage I 0.929336194 TCGA-F1-6874-01A Stage I 0.600310017 TCGA-BR-6710-01A Stage I 0.5014603 TCGA-HF-7131-01A Stage I 0.8002986 TCGA-D7-6822-01A Stage I 4.448854983 TCGA-BR-8678-01A Stage I 2.936808123 TCGA-CG-4437-01A Stage II 1.503378 TCGA-CD-5803-01A Stage II 1.520788808 TCGA-D7-6527-01A Stage II 0.685830271 TCGA-CD-5799-01A Stage II 0.2614236 TCGA-RD-A8N9-01A Stage II 2.059083679 TCGA-BR-7704-01A Stage II 0.798481387 TCGA-CD-5798-01A Stage II 1.699647 TCGA-CG-4305-01A Stage II 1.293942682 TCGA-HF-7132-01A Stage II 0.9201286 TCGA-CG-5717-01A Stage II 0.556331697 TCGA-KB-A93J-01A Stage II 0.875837139 TCGA-CD-8524-01A Stage II 0.559488 TCGA-CD-8532-01A Stage II 0.759960175 TCGA-CG-5718-01A Stage II 1.857829277 TCGA-CD-5813-01A Stage II 1.250586 TCGA-VQ-A924-01A Stage II 0.434719963 TCGA-CD-8530-01A Stage II 1.241600265 TCGA-CD-8534-01A Stage II 1.07492996 TCGA-D7-6524-01A Stage II 1.292202 TCGA-CD-8533-01A Stage II 2.163831687 TCGA-BR-7197-01A Stage II 3.026373225 TCGA-CD-8527-01A Stage II 0.598441536 TCGA-BR-4279-01A Stage II 1.266757 TCGA-BR-8286-01A Stage II 1.413375329 TCGA-VQ-A8PB-01A Stage II 0.7970482 TCGA-CG-5723-01A Stage II 3.580079 TCGA-CD-5800-01A Stage II 0.249893375 TCGA-MX-A663-01A Stage II 1.295718 TCGA-F1-A72C-01A Stage II 0.739025063 TCGA-CD-A489-01A Stage II 2.131037267 TCGA-BR-6852-01A Stage II 0.877571057 TCGA-IN-A6RN-01A Stage II 1.513373245 TCGA-BR-A44T-01A Stage II 2.171675372 TCGA-HU-A4GF-01A Stage II 1.36954 TCGA-CD-A4MG-01A Stage II 0.408558629 TCGA-VQ-A8E3-01A Stage II 3.081853876 TCGA-HU-A4GP-01A Stage II 0.435035046 TCGA-BR-A4J6-01A Stage II 1.097417 TCGA-BR-A4J9-01A Stage II 2.434034579 TCGA-BR-6454-01A Stage II 0.725018201 TCGA-MX-A666-01A Stage II 0.818763254 TCGA-VQ-AA6G-01A Stage II 0.3521321 TCGA-BR-8487-01A Stage II 0.223323997 TCGA-BR-6801-01A Stage II 1.038954242 TCGA-VQ-A8P5-01A Stage II 0.811619091 TCGA-BR-6457-01A Stage II 1.561369466 TCGA-CD-A48A-01A Stage II 0.989641278 TCGA-BR-6803-01A Stage II 1.879246 TCGA-BR-6453-01A Stage II 0.4805631 TCGA-CD-A486-01A Stage II 0.240164937 TCGA-CD-A4MH-01A Stage II 1.774527356 TCGA-HU-A4GT-01A Stage II 0.4896677 TCGA-BR-7715-01A Stage II 3.593798197 TCGA-FP-8099-01A Stage II 0.845822154 TCGA-D7-8573-01A Stage II 0.44381074 TCGA-BR-6707-01A Stage II 0.264970572 TCGA-BR-8365-01A Stage II 2.311381128 TCGA-BR-6566-01A Stage II 0.47232569 TCGA-BR-6452-01A Stage II 0.578756363 TCGA-HU-8604-01A Stage II 0.609605188 TCGA-BR-8366-01A Stage II 1.329605209 TCGA-IN-AB1X-01A Stage II 0.4308684 TCGA-IN-A7NT-01A Stage II 2.91324794 TCGA-IN-8462-01A Stage II 0.932895484 TCGA-CG-4475-01A Stage II 1.16838046 TCGA-BR-7851-01A Stage II 0.7227592 TCGA-EQ-8122-01A Stage II 1.057794938 TCGA-D7-8572-01A Stage II 1.556629128 TCGA-B7-A5TN-01A Stage II 0.8008817 TCGA-BR-A4J7-01A Stage II 1.886256963 TCGA-HU-A4G8-01A Stage II 0.608693755 TCGA-HU-A4H4-01A Stage II 1.586466 TCGA-VQ-A8P8-01A Stage II 1.443544263 TCGA-HU-8602-01A Stage II 0.2581841 TCGA-B7-A5TJ-01A Stage II 0.9022934 TCGA-BR-8588-01A Stage II 1.210256789 TCGA-BR-7901-01A Stage II 1.123011332 TCGA-BR-6458-01A Stage II 1.496269 TCGA-HU-A4G2-01A Stage II 0.5004366 TCGA-VQ-AA6F-01A Stage II 0.9762021 TCGA-BR-7722-01A Stage II 0.713876713 TCGA-KB-A93H-01A Stage II 0.3558624 TCGA-IN-7806-01A Stage II 0.622760413 TCGA-HU-A4HB-01A Stage II 0.751186513 TCGA-VQ-A8PO-01A Stage II 0.6459504 TCGA-FP-7829-01A Stage II 0.861595145 TCGA-D7-A6EV-01A Stage II 0.3882407 TCGA-BR-8060-01A Stage II 2.865429236 TCGA-BR-7716-01A Stage II 1.385922 TCGA-FP-8211-01A Stage II 0.423115279 TCGA-D7-6815-01A Stage II 0.627507871 TCGA-BR-6563-01A Stage II 1.319872 TCGA-HU-A4GD-01A Stage II 0.801933961 TCGA-BR-6455-01A Stage II 0.4912628 TCGA-D7-A4YX-01A Stage II 1.383958 TCGA-HU-A4GU-01A Stage II 0.2087343 TCGA-BR-8295-01A Stage II 0.831938124 TCGA-BR-8682-01A Stage II 1.658057 TCGA-D7-8579-01A Stage II 2.304196067 TCGA-BR-8291-01A Stage II 1.184943 TCGA-VQ-A94U-01A Stage II 0.815542092 TCGA-BR-8081-01A Stage II 0.732473344 TCGA-BR-6565-01A Stage II 0.8861372 TCGA-CD-A48C-01A Stage II 1.065703096 TCGA-D7-A747-01A Stage II 2.958433846 TCGA-D7-A4Z0-01A Stage II 1.490160741 TCGA-BR-6456-01A Stage II 2.03242 TCGA-HU-A4G3-01A Stage II 0.50014841 TCGA-CD-A487-01A Stage II 1.826746208 TCGA-IN-8663-01A Stage II 1.634578 TCGA-BR-8381-01A Stage II 1.10347197 TCGA-BR-4280-01A Stage III 0.3758072 TCGA-BR-8059-01A Stage III 1.130189008 TCGA-R5-A7ZR-01A Stage III 0.724968408 TCGA-D7-6525-01A Stage III 3.780733 TCGA-MX-A5UG-01A Stage III 1.571898823 TCGA-HU-A4HD-01A Stage III 2.582628 TCGA-FP-8631-01A Stage III 0.683774921 TCGA-D7-6520-01A Stage III 1.688533 TCGA-D7-A6EZ-01A Stage III 2.411207 TCGA-RD-A8N6-01A Stage III 1.745753522 TCGA-CG-5734-01A Stage III 0.570689422 TCGA-D7-A74A-01A Stage III 0.3577528 TCGA-BR-4361-01A Stage III 0.779057622 TCGA-D7-6526-01A Stage III 0.933817416 TCGA-HU-A4GY-01A Stage III 1.149567403 TCGA-CG-4441-01A Stage III 0.5399682 TCGA-VQ-A91U-01A Stage III 1.009765606 TCGA-RD-A8N4-01A Stage III 2.998312461 TCGA-D7-A6EX-01A Stage III 6.050786 TCGA-CD-8528-01A Stage III 0.191428542 TCGA-VQ-A8P2-01A Stage III 0.26317772 TCGA-BR-8484-01A Stage III 0.619402336 TCGA-SW-A7EB-01A Stage III 0.653730759 TCGA-VQ-A8PC-01A Stage III 0.962254692 TCGA-R5-A7ZE-01B Stage III 1.211488 TCGA-VQ-A923-01A Stage III 0.791169144 TCGA-VQ-A8DU-01A Stage III 1.997070671 TCGA-BR-4253-01A Stage III 1.54830758 TCGA-MX-A5UJ-01A Stage III 1.99270593 TCGA-D7-8575-01A Stage III 0.711934132 TCGA-FP-A4BF-01A Stage III 1.210351272 TCGA-CD-8535-01A Stage III 3.448642876 TCGA-VQ-A91V-01A Stage III 1.807529 TCGA-RD-A8N5-01A Stage III 1.337447623 TCGA-VQ-AA69-01A Stage III 2.294108 TCGA-CD-5801-01A Stage III 0.316455779 TCGA-RD-A8NB-01A Stage III 1.813913301 TCGA-BR-8373-01A Stage III 1.053330298 TCGA-VQ-A8P3-01A Stage III 1.277491098 TCGA-RD-A7BS-01A Stage III 1.63620727 TCGA-BR-6802-01A Stage III 2.237238626 TCGA-CD-8525-01A Stage III 0.538279058 TCGA-BR-8483-01A Stage III 1.070246571 TCGA-CD-8531-01A Stage III 0.7905349 TCGA-D7-8574-01A Stage III 1.064130323 TCGA-BR-A4J5-01A Stage III 2.087054183 TCGA-D7-5578-01A Stage III 0.654636 TCGA-VQ-A925-01A Stage III 0.6858951 TCGA-VQ-A91Z-01A Stage III 1.464593 TCGA-BR-6564-01A Stage III 1.496590862 TCGA-CD-8526-01A Stage III 2.75320033 TCGA-HU-A4H6-01A Stage III 0.481619541 TCGA-VQ-A91K-01A Stage III 0.701677 TCGA-D7-6818-01A Stage III 0.6201269 TCGA-VQ-A8PU-01A Stage III 0.5169809 TCGA-HU-8249-01A Stage III 1.102356332 TCGA-B7-A5TK-01A Stage III 2.790247958 TCGA-D7-5577-01A Stage III 0.47690858 TCGA-VQ-AA6D-01A Stage III 0.644128773 TCGA-FP-8210-01A Stage III 2.030933 TCGA-BR-7959-01A Stage III 1.544005 TCGA-CG-4444-01A Stage III 0.835763222 TCGA-VQ-A8E0-01A Stage III 0.218735056 TCGA-BR-A44U-01A Stage III 0.739773439 TCGA-BR-A4IV-01A Stage III 2.144946 TCGA-BR-8683-01A Stage III 3.050917169 TCGA-D7-A4YU-01A Stage III 2.063639048 TCGA-BR-8677-01A Stage III 2.038649289 TCGA-RD-A8MV-01A Stage III 1.201460603 TCGA-BR-8371-01A Stage III 2.8776404 TCGA-D7-A6EY-01A Stage III 1.43467 TCGA-RD-A8N0-01A Stage III 1.058342519 TCGA-VQ-A91S-01A Stage III 0.564048064 TCGA-BR-A4J4-01A Stage III 2.170208386 TCGA-D7-8576-01A Stage III 0.332246598 TCGA-VQ-A8PF-01A Stage III 0.6814642 TCGA-VQ-A8DT-01A Stage III 0.485804027 TCGA-BR-8369-01A Stage III 1.814888522 TCGA-BR-8077-01A Stage III 0.606516781 TCGA-VQ-A94T-01A Stage III 0.6754407 TCGA-BR-8690-01A Stage III 1.091391477 TCGA-BR-7723-01A Stage III 0.5481488 TCGA-VQ-A91E-01A Stage III 0.3936808 TCGA-VQ-A91A-01A Stage III 1.374345 TCGA-VQ-A8PE-01A Stage III 1.060654 TCGA-BR-A4PF-01A Stage III 0.559682426 TCGA-BR-7958-01A Stage III 1.416865472 TCGA-BR-6709-01A Stage III 1.304852212 TCGA-BR-8589-01A Stage III 0.299837005 TCGA-VQ-A8PK-01A Stage III 0.948315669 TCGA-D7-8570-01A Stage III 0.545300493 TCGA-3M-AB47-01A Stage III 1.098889176 TCGA-F1-A448-01A Stage III 0.6829584 TCGA-VQ-A91X-01A Stage III 0.359045889 TCGA-HU-A4H2-01A Stage III 0.35304878 TCGA-BR-6705-01A Stage III 1.038298247 TCGA-VQ-A8PH-01A Stage III 0.567102886 TCGA-BR-8058-01A Stage III 1.000026 TCGA-BR-8592-01A Stage III 2.370944 TCGA-BR-8676-01A Stage III 0.868585786 TCGA-RD-A8N1-01A Stage III 1.309181 TCGA-HU-8608-01A Stage III 0.9521978 TCGA-R5-A805-01A Stage III 0.904367341 TCGA-BR-A4J8-01A Stage III 1.66036106 TCGA-VQ-A8E2-01A Stage III 2.180529292 TCGA-BR-8686-01A Stage III 1.158944114 TCGA-IN-A7NU-01A Stage III 0.986536146 TCGA-VQ-A927-01A Stage III 0.999568385 TCGA-BR-8367-01A Stage III 1.733730397 TCGA-IP-7968-01A Stage III 1.18188 TCGA-RD-A8MW-01A Stage III 0.866863096 TCGA-HU-A4GC-01A Stage III 0.839668959 TCGA-BR-A4QL-01A Stage III 0.1216131 TCGA-VQ-AA64-01A Stage III 1.146117 TCGA-VQ-AA6J-01A Stage III 0.6295464 TCGA-BR-A4CR-01A Stage III 0.311930067 TCGA-VQ-A91Y-01A Stage III 2.313837322 TCGA-HU-A4H0-01A Stage III 0.1954525 TCGA-VQ-AA68-01A Stage III 1.222582 TCGA-FP-7916-01A Stage III 1.040138 TCGA-B7-A5TI-01A Stage III 0.512300181 TCGA-HU-A4H3-01A Stage III 3.259066475 TCGA-VQ-A91D-01A Stage III 0.2015516 TCGA-VQ-A94O-01A Stage III 0.926945262 TCGA-HU-A4GX-01A Stage III 1.342377967 TCGA-BR-8384-01A Stage III 2.763102 TCGA-BR-8361-01A Stage III 0.582259393 TCGA-BR-8080-01A Stage III 1.935243589 TCGA-BR-8485-01A Stage III 1.115993514 TCGA-BR-8372-01A Stage III 0.984379128 TCGA-VQ-A8PD-01A Stage III 1.149639287 TCGA-BR-8590-01A Stage III 2.301026036 TCGA-BR-8297-01A Stage III 2.327849306 TCGA-BR-8382-01A Stage III 0.996506592 TCGA-HF-A5NB-01A Stage III 0.4444563 TCGA-BR-8296-01A Stage III 0.810985036 TCGA-BR-8364-01A Stage III 1.966567674 TCGA-VQ-AA6A-01A Stage III 0.845389025 TCGA-FP-7998-01A Stage III 1.685827 TCGA-BR-8687-01A Stage III 0.6432743 TCGA-HU-A4GQ-01A Stage III 1.216920374 TCGA-BR-8284-01A Stage III 1.044673975 TCGA-CG-4476-01A Stage III 1.986112067 TCGA-VQ-AA6K-01A Stage III 1.177972 TCGA-BR-A4CS-01A Stage III 0.9709531 TCGA-FP-A8CX-01A Stage III 0.3879725 TCGA-BR-8591-01A Stage III 0.6849949 TCGA-HU-A4GJ-01A Stage III 0.834695788 TCGA-ZQ-A9CR-01A Stage III 0.622380483 TCGA-BR-8380-01A Stage III 2.018217 TCGA-VQ-A91N-01A Stage IV 1.301181 TCGA-BR-7196-01A Stage IV 1.557080958 TCGA-CG-5732-01A Stage IV 0.3293246 TCGA-R5-A7O7-01A Stage IV 0.540326529 TCGA-CG-5724-01A Stage IV 2.231384219 TCGA-BR-7717-01A Stage IV 0.7319209 TCGA-R5-A7ZF-01A Stage IV 2.393267104 TCGA-CG-4301-01A Stage IV 2.218155132 TCGA-CG-5722-01A Stage IV 0.708129097 TCGA-CG-5716-01A Stage IV 0.468816 TCGA-VQ-A8PQ-01A Stage IV 1.415177765 TCGA-VQ-A922-01A Stage IV 1.035280788 TCGA-CG-4438-01A Stage IV 2.272986408 TCGA-VQ-A928-01A Stage IV 0.834883 TCGA-CG-5719-01A Stage IV 0.58830405 TCGA-VQ-A8E7-01B Stage IV 0.6447984 TCGA-BR-7957-01A Stage IV 1.9686025 TCGA-BR-4368-01A Stage IV 2.805810457 TCGA-CG-5721-01A Stage IV 2.216479938 TCGA-BR-8680-01A Stage IV 1.160640439 TCGA-VQ-A8DZ-01A Stage IV 0.5019263 TCGA-CG-4440-01A Stage IV 2.845620371 TCGA-IN-A7NR-01A Stage IV 0.755740942 TCGA-VQ-A8PP-01A Stage IV 1.196001 TCGA-RD-A7BT-01A Stage IV 0.767497553 TCGA-CG-4460-01A Stage IV 0.65891134 TCGA-VQ-A8PM-01A Stage IV 0.897091313 TCGA-CD-8529-01A Stage IV 1.044818087 TCGA-VQ-A91Q-01A Stage IV 1.324762039 TCGA-CG-4306-01A Stage IV 1.381822735 TCGA-HF-7133-01A Stage IV 3.707496764 TCGA-D7-A748-01A Stage IV 1.029959683 TCGA-CG-4465-01A Stage IV 0.683991979 TCGA-VQ-A8PJ-01A Stage IV 0.682241791 TCGA-CG-4469-01A Stage IV 0.7742638 TCGA-R5-A7ZI-01A Stage IV 0.12340956 TCGA-BR-8289-01A Stage IV 0.7970905 TCGA-CG-4462-01A Stage IV 1.44904143
代码：
library(ggpubr)
inputFile <- "input.txt" # 输入文件
outFile <- "vioplot.pdf" # 输出文件
setwd("") # 工作目录
# 读取
rt <- read.table(inputFile, header = T, sep = "\t", check.names = F)
x <- colnames(rt)[2]
y <- colnames(rt)[3]
colnames(rt) <- c("id", "Type", "Expression")
# 设置比较组
group <- levels(factor(rt$Type))
rt$Type <- factor(rt$Type, levels = group)
comp <- combn(group, 2) # combn表示从“group向量”中任意挑选出“2个”元素，将所有可能的情况组成新的矩阵。用于分组之间两两比较。
my_comparisons <- list()
for(i in 1:ncol(comp)){
my_comparisons[[i]] <- comp[,i]
}
# 绘制
p <- ggviolin(rt, x = "Type", y = "Expression", fill = "Type",
xlab = x,
ylab = y,
legend.title = x,
add = "boxplot",
add.params = list(fill = "white")) +
stat_compare_means(comparisons = my_comparisons) # 显示p值数值
#stat_compare_means(comparisons = my_comparisons, symnum.args = list(cutpoints = c(0, 0.001, 0.01, 0.05, 1), symbols = c("***", "**", "*", "ns")), label = "p.signif") # 显示p值符号
# 输出图片文件
pdf(file = outFile, width = 6, height = 5)
print(p)
dev.off()
2. 多个基因表达_癌症组织vs正常组织
输入数据：
ID Type SEMA3A SEMA3B SEMA3C SEMA3D SEMA3E SEMA3F SEMA3G TCGA-HU-A4GY-11A Normal 3.661119844 3.018973244 5.53455774 1.078964861 2.747022902 2.931838304 2.546564425 TCGA-IP-7968-11A Normal 0.719789769 2.768937911 2.555889615 0.32180929 0.726514401 5.465899753 1.06982675 TCGA-CG-5721-11A Normal 0.309808074 3.329437454 2.576201484 0.439781398 0.551606481 3.63934768 2.094286299 TCGA-HU-A4GH-11A Normal 3.094985227 3.716985871 5.537263729 0.932725326 1.903352116 2.666218686 2.169933062 TCGA-HU-A4GP-11A Normal 3.219241 2.879605 5.69509 1.2209 2.146337 2.277748 1.945595 TCGA-BR-6454-11A Normal 1.202934811 3.777363445 3.341892129 0.555995759 1.14398083 3.987617667 1.433447418 TCGA-CG-5730-11A Normal 0.638117081 3.826906181 1.738406049 0.603697219 0.402600981 3.000365148 1.05052569 TCGA-HU-A4GN-11A Normal 2.452111 3.451706 4.350185 0.9964425 1.535583 2.11437 1.053774 TCGA-CG-5722-11A Normal 1.039763271 4.302667656 3.665872348 0.797790004 0.860207944 4.249355765 1.966670829 TCGA-FP-7829-11A Normal 3.308123 3.515444 4.672184 1.437351 3.050688 2.741295 3.133283 TCGA-IN-AB1X-11A Normal 0.6330329 1.379456 2.191349 0.09490068 0.4003732 5.415253 1.023158 TCGA-BR-7704-11A Normal 2.301362 4.275577 4.36339 1.024271 1.153101 3.356964 2.580009 TCGA-BR-7703-11A Normal 0.4974569 4.084672 3.281543 0.5557823 0.9772476 4.199041 2.132408 TCGA-BR-6453-11A Normal 0.705235985 3.623207141 2.600548748 0.734845942 0.457095487 3.392416475 1.731103629 TCGA-BR-7717-11A Normal 1.457473117 3.040889546 2.994016011 0.70880988 0.630026752 3.549909264 1.604783004 TCGA-BR-7716-11A Normal 1.21344 4.022319 3.899888 0.9301745 1.271382 4.295031 2.028455 TCGA-IN-7806-11A Normal 0.4003166 0.9114159 1.029266 0.0384844 0.2845323 5.700332 1.213146 TCGA-HU-A4GC-11A Normal 2.878481206 3.663600233 5.143618289 1.004935936 1.106747735 1.691826252 1.943762447 TCGA-CG-5734-11A Normal 0.271120614 4.160396917 2.304790606 0.33381226 0.681187213 3.02184377 1.721724228 TCGA-HU-8238-11A Normal 0.2060026 4.995417 2.332126 0.2168459 0.2965699 2.434923 0.9250856 TCGA-CG-5728-11A Normal 0.647246478 3.177694481 2.181741993 0.719273186 1.02287011 3.879007446 1.631657892 TCGA-BR-6802-11A Normal 0.47559702 2.209018008 2.717015666 0.439098439 0.722256665 2.076367346 0.801915333 TCGA-HU-A4HB-11A Normal 3.069671 3.317084 5.967813 2.780674 1.591952 2.441388 1.916547 TCGA-BR-6457-11A Normal 0.465186383 4.154019201 2.680528018 0.732635645 0.576233656 3.818347128 1.956002866 TCGA-BR-7851-11A Normal 0.492046416 4.383190666 3.329537268 0.462517677 0.67456117 3.07405277 1.50868973 TCGA-FP-7735-11A Normal 3.143004 3.640905 5.110441 1.222668 2.618905 2.233282 2.157939 TCGA-BR-8060-11A Normal 1.695557589 3.564547507 4.13280937 0.833374862 1.257504977 2.798434351 1.89291008 TCGA-IN-AB1V-11A Normal 1.491206 1.480384 3.033261 0.2717649 1.224155 5.528908 1.193253 TCGA-BR-7715-11A Normal 0.9602919 3.323168 2.543165 1.056427 0.4032764 3.471566 2.49417 TCGA-CG-5733-11A Normal 0.530264493 3.470837153 2.301449745 0.669465129 0.971639413 3.685453933 1.977175062 TCGA-CG-5720-11A Normal 0.304557827 4.315205684 1.869467474 0.473252267 0.130251883 3.5011748 1.531668647 TCGA-IN-8663-11A Normal 0.487552529 0.676971888 1.099642548 0.045253549 0.128370359 5.26582918 0.348704113 TCGA-D7-5577-01A Tumor 0.47690858 4.297823133 3.304884099 0.080311232 0.065753996 3.166858468 0.611160518 TCGA-D7-6818-01A Tumor 0.6201269 1.121709 2.353106 0.5477714 0.2466362 4.753481 1.704684 TCGA-BR-4280-01A Tumor 0.3758072 2.404825 3.383737 0.01183228 0.005666635 3.43121 0.4773466 TCGA-D7-8572-01A Tumor 1.556629128 2.812997577 3.468085397 0.983905862 0.313731602 2.89554401 1.785540081 TCGA-VQ-A91Z-01A Tumor 1.464593 4.355924 2.829831 1.366626 0.3527911 5.697085 0.3341439 TCGA-HU-A4HD-01A Tumor 2.582628 3.862809 3.314509 1.250642 1.609892 3.455356 1.44399 TCGA-D7-8573-01A Tumor 0.44381074 4.599663779 0.934843472 0.064755151 0.132945557 2.625730761 0.383273035 TCGA-BR-7959-01A Tumor 1.544005 2.800879 4.386488 0.6053695 1.475969 3.221628 2.273923 TCGA-BR-8679-01A Tumor 1.286488303 2.219615004 3.482133827 0.107739017 0.381672106 2.822825341 1.753867145 TCGA-CG-5726-01A Tumor 0.1253805 3.138453 1.15533 0.003168569 0.01882528 2.261293 0.6888249 TCGA-BR-6453-01A Tumor 0.4805631 1.929144 2.374879 0.3652917 0.06131856 3.058088 2.847552 TCGA-BR-A4QL-01A Tumor 0.1216131 2.009781 2.750043 0.004207799 0.01253166 1.827618 0.4355719 TCGA-VQ-AA6A-01A Tumor 0.845389025 3.599872118 4.301761883 1.992675001 2.548485832 2.246683346 1.061344727 TCGA-HF-7132-01A Tumor 0.9201286 3.090548 3.510468 0.582881 0.7863224 3.166648 1.926389 TCGA-BR-A4IV-01A Tumor 2.144946 2.966931 5.59729 1.370192 1.847926 2.718832 2.529109 TCGA-CG-5718-01A Tumor 1.857829277 2.425998843 1.087852372 0.073718312 2.342333677 4.520334811 1.756124821 TCGA-BR-8296-01A Tumor 0.810985036 3.836270275 2.696872141 0.63432361 0.541882377 4.441629059 2.188251342 TCGA-R5-A7ZR-01A Tumor 0.724968408 1.770838893 3.268238381 0.056138673 0.711069162 2.222319469 0.560518654 TCGA-BR-8680-01A Tumor 1.160640439 3.482876516 4.031267716 0.046598621 0.131717012 2.429506489 0.941816399 TCGA-VQ-A8P2-01A Tumor 0.26317772 2.80880905 3.740855395 0.006378034 0.026484424 3.294496549 1.008795474 TCGA-CD-8533-01A Tumor 2.163831687 0.970335248 4.552992815 1.637156078 0.086176925 2.953081045 1.676532525 TCGA-RD-A8N2-01A Tumor 3.535827105 2.515268697 6.090355355 0.155653723 2.419828048 1.974399108 1.653248719 TCGA-VQ-A92D-01A Tumor 0.30548 3.649859 3.438911 0.01026218 0 3.001307 1.083134 TCGA-HU-A4GT-01A Tumor 0.4896677 2.603637 3.046733 0.01958106 0.6613976 2.764571 0.626798 TCGA-ZA-A8F6-01A Tumor 2.019519 3.275653 4.666158 0.3454467 0.4064711 2.452359 1.869219 TCGA-D7-A74A-01A Tumor 0.3577528 3.390495 4.074864 0.09192331 2.73205 2.309341 0.3718595 TCGA-IN-A7NR-01A Tumor 0.755740942 2.703438686 3.826227798 0.373109823 0.618896675 4.07819948 1.367237757 TCGA-HU-A4H2-01A Tumor 0.35304878 3.555129947 3.160883973 0.118498064 0.122655655 2.590239112 1.103251755 TCGA-BR-6456-01A Tumor 2.03242 1.376818 4.37951 0.3750618 0.6652706 3.69372 1.78324 TCGA-CG-4442-01A Tumor 1.55303475 3.842905284 3.106845755 0.147287068 0.130068441 2.550664372 1.549380798 TCGA-CD-8524-01A Tumor 0.559488 1.901373 4.253283 0.5063804 0.163215 2.630983 2.331275 TCGA-VQ-A8PO-01A Tumor 0.6459504 2.488975 2.269449 0.1261328 0.005820746 3.093436 1.18 TCGA-BR-7717-01A Tumor 0.7319209 1.646986 2.464738 0.1804089 0.3870062 2.93681 1.765642 TCGA-CG-4475-01A Tumor 1.16838046 3.72184425 4.350650109 0.706481365 1.424577848 3.364569583 1.10183585 TCGA-BR-4369-01A Tumor 2.185663233 2.271713311 5.374062761 1.324504567 0.164073159 1.846984413 1.092383859 TCGA-HU-A4GP-01A Tumor 0.435035046 4.640004633 0.808737932 0.121229802 0.054619687 4.057116484 1.761360893 TCGA-VQ-A94R-01A Tumor 0.8761634 2.649888 3.886337 0.284255 0.3247867 3.33098 2.211315 TCGA-VQ-A91E-01A Tumor 0.3936808 5.752307 2.79411 0.1851439 0.04271142 4.24143 0.8209434 TCGA-HU-A4GD-01A Tumor 0.801933961 1.976661536 2.878227565 1.407407347 0.457359281 2.341225593 0.695133639 TCGA-FP-8211-01A Tumor 0.423115279 4.212427961 2.308385341 0.217637023 0.584356976 3.658357318 0.864737934 TCGA-D7-A747-01A Tumor 2.958433846 1.935042314 5.361883426 0.283566173 2.316302472 1.899782453 1.229607195 TCGA-KB-A93G-01A Tumor 0.527477971 1.856737647 3.251949066 0.870613018 0.724239271 3.997242724 1.977862955 TCGA-RD-A8MV-01A Tumor 1.201460603 2.795717999 3.681823829 0.161389883 0.079381474 4.183792663 1.960175237 TCGA-BR-4256-01A Tumor 2.086367066 1.607329154 4.192980179 0.697505737 1.352922853 3.030670916 1.613402186 TCGA-FP-7735-01A Tumor 0.6413326 2.257085 1.174668 0.120885 1.869108 5.094119 1.812654 TCGA-VQ-A8PK-01A Tumor 0.948315669 3.640310243 3.935124256 0.786960837 4.766284924 3.689627042 0.725814848 TCGA-BR-7707-01A Tumor 0.2068636 3.61934 1.394923 0.08485049 0.008674976 3.950335 0.9963288 TCGA-IN-A6RS-01A Tumor 0.3461303 0.8250202 2.156692 0.002688006 0.09936001 3.803562 0.6397637 TCGA-D7-6519-01A Tumor 4.251745478 2.898041884 3.794378626 0.649938872 1.099310864 2.768828225 0.783644198 TCGA-CG-4440-01A Tumor 2.845620371 2.68653978 4.374942085 1.461571258 1.950574065 1.916348673 0.654805911 TCGA-BR-8487-01A Tumor 0.223323997 3.580216253 2.923758686 0.067707959 0.036796012 3.488818117 1.071497566 TCGA-VQ-A94U-01A Tumor 0.815542092 3.242250294 2.291645493 0.34306865 0.375054028 3.68174425 2.220171787 TCGA-CG-5717-01A Tumor 0.556331697 2.166505616 2.085678311 0.265216773 0.539329198 5.476761711 1.638659157 TCGA-BR-A4CR-01A Tumor 0.311930067 0.320176882 2.572932144 1.723686234 0.485327185 3.493720551 0.548486249 TCGA-HU-8249-01A Tumor 1.102356332 0.562543358 4.370634549 0.090980029 0.143505159 3.406393032 1.081255586 TCGA-BR-6454-01A Tumor 0.725018201 2.948267512 3.846877021 0.164451018 1.378785231 4.063344031 1.666204038 TCGA-BR-8295-01A Tumor 0.831938124 0.997926343 0.866387587 0.382427466 0.178438817 2.593378282 1.55321713 TCGA-BR-7722-01A Tumor 0.713876713 5.299977479 2.07342942 0.344730092 1.004749543 3.008241897 1.301644112 TCGA-HU-A4HB-01A Tumor 0.751186513 3.172507533 3.429691496 0.986387307 1.557239772 3.028828681 1.722753138 TCGA-BR-7958-01A Tumor 1.416865472 2.529843541 3.900949919 0.40954048 1.692452296 4.307953235 0.993534243 TCGA-BR-7197-01A Tumor 3.026373225 1.162868379 2.486507839 1.568384765 0.610856593 4.594310688 1.608695373 TCGA-VQ-A94P-01A Tumor 2.906654017 3.274846305 5.603475664 0.21815934 2.651620943 3.089495422 2.657682487 TCGA-D7-8575-01A Tumor 0.711934132 5.06763848 2.577858071 0.188713031 0.432424974 2.146351218 1.020224705 TCGA-VQ-A8E0-01A Tumor 0.218735056 3.429634421 2.859741135 0.139581713 2.530508501 4.243596026 1.369454984 TCGA-VQ-A8PP-01A Tumor 1.196001 0.5114453 2.741775 0.2560013 0.1352637 2.819331 0.7891131 TCGA-BR-8372-01A Tumor 0.984379128 2.693621943 2.272315754 0.085407425 0.153479122 2.459249228 0.491329664 TCGA-VQ-A91Y-01A Tumor 2.313837322 2.696111937 5.157814604 0.425979481 1.442474 2.746463364 1.437277334 TCGA-IN-A6RL-01A Tumor 1.197591895 4.228484862 2.542367344 0.562425878 0.986548593 3.713471004 1.128252592 TCGA-CG-5732-01A Tumor 0.3293246 3.836962 2.774348 0.362716 1.805546 3.755871 1.267335 TCGA-RD-A8MW-01A Tumor 0.866863096 2.158388638 3.432791058 0.142502447 2.274165995 3.304226674 0.88213275 TCGA-KB-A6F7-01A Tumor 0.766425706 1.532141876 2.878310856 0.966574512 0.062076036 2.881132332 0.992486874 TCGA-BR-8382-01A Tumor 0.996506592 3.881628818 3.10721787 0.141069734 0.187429062 2.810136831 1.476122332 TCGA-BR-8060-01A Tumor 2.865429236 1.829052848 2.570229591 0.93762131 1.020865559 3.227587008 2.481575116 TCGA-HU-A4GF-01A Tumor 1.36954 2.616538 3.149865 0.009429756 0.5326351 4.10749 1.721296 TCGA-R5-A7ZI-01A Tumor 0.12340956 2.606398211 0.377489707 0.029645556 0.014243327 3.061041955 0.708972103 TCGA-BR-8588-01A Tumor 1.210256789 2.193493753 3.780099901 0.331248905 0.428119079 3.030366063 2.135880995 TCGA-CD-5801-01A Tumor 0.316455779 3.477606162 1.2111961 0.026577541 0.005331323 3.433576874 1.012249724 TCGA-CD-5800-01A Tumor 0.249893375 2.340270994 0.784831104 0.035523563 0.042340269 2.911309448 1.68071809 TCGA-CG-4462-01A Tumor 1.44904143 3.55664507 3.393401336 0.525955385 1.565791801 3.343363542 2.072490099 TCGA-CD-8530-01A Tumor 1.241600265 4.177242607 2.602953128 0.809914 0.519255519 3.788047925 2.916830639 TCGA-VQ-A8PX-01A Tumor 0.391461954 4.230095184 1.720071972 0.03215389 0.539633486 3.560325437 0.990870372 TCGA-D7-8578-01A Tumor 1.868535316 3.217099419 4.53553166 1.141669634 1.91060132 3.175968626 1.092957136 TCGA-BR-6458-01A Tumor 1.496269 3.357097 2.781342 0.3707743 0.3178205 3.019827 2.318389 TCGA-VQ-A8PB-01A Tumor 0.7970482 2.601381 5.064992 0.2179054 0.006783045 2.441644 0.7530935 TCGA-D7-6822-01A Tumor 4.448854983 1.495886649 2.044834322 2.831964999 0.710417035 6.264131354 1.461375541 TCGA-BR-8284-01A Tumor 1.044673975 1.6831893 3.649188289 0.137789976 2.550900258 3.731391849 2.224688548 TCGA-3M-AB47-01A Tumor 1.098889176 1.593390687 4.378377339 0.466753154 0.234701274 3.465388485 2.950319564 TCGA-BR-8381-01A Tumor 1.10347197 2.039780084 2.383554936 0.194117557 1.255384704 2.745057267 1.286031191 TCGA-BR-4191-01A Tumor 1.187516384 2.120231807 3.939793287 0.299720734 0.529625425 4.449225049 1.042543128 TCGA-MX-A666-01A Tumor 0.818763254 2.828879867 1.86525394 0.615115227 0.098391325 3.223517711 2.336953736 TCGA-CD-A486-01A Tumor 0.240164937 3.269475173 2.068928076 0.343801983 0.254873335 3.748738017 0.970921936 TCGA-BR-8077-01A Tumor 0.606516781 1.189708945 2.676699421 0.096495714 0.198126851 3.955756507 1.659799108 TCGA-MX-A663-01A Tumor 1.295718 3.325876 4.187002 0.8371021 0.7800354 3.583415 3.324734 TCGA-R5-A7O7-01A Tumor 0.540326529 2.007602718 1.407062353 0.099769238 0.234422785 3.750046436 0.701671031 TCGA-VQ-A8DZ-01A Tumor 0.5019263 4.120438 2.570922 0.7100363 0.4869014 3.36606 1.345823 TCGA-BR-A44T-01A Tumor 2.171675372 2.605084599 4.07076203 0.753088148 1.585379257 1.712235874 1.468598108 TCGA-HU-A4H6-01A Tumor 0.481619541 3.039718863 1.493515223 0.21020782 0.061288874 3.745157222 2.055125249 TCGA-BR-A4CS-01A Tumor 0.9709531 1.914282 2.320955 0.07697631 0.9519857 3.464356 1.661869 TCGA-CG-4438-01A Tumor 2.272986408 2.327628537 2.88348591 1.338690609 0.472171834 1.8378065 0.572066979 TCGA-RD-A7BW-01A Tumor 2.36891042 2.629037232 4.676220863 0.65327058 1.157029412 2.885989338 1.397103162 TCGA-D7-8570-01A Tumor 0.545300493 2.744661281 2.684238423 0.107452084 0.203850643 4.26102742 0.974975104 TCGA-BR-4368-01A Tumor 2.805810457 3.039543155 4.030005123 0.673127476 0.808959605 2.103774633 1.796570402 TCGA-CG-5720-01A Tumor 0.4694241 2.370338 2.524386 0.09574594 0.01679771 3.37344 2.011199 TCGA-D7-8579-01A Tumor 2.304196067 3.055137913 4.479091748 0.523321821 1.662610192 2.908841933 2.338908589 TCGA-IN-A6RO-01A Tumor 0.6163783 1.590592 4.669849 0.002290095 1.09423 2.889296 0.4166468 TCGA-VQ-AA69-01A Tumor 2.294108 1.24858 1.686808 0.0472187 0.002604315 4.521007 0.4642136 TCGA-IP-7968-01A Tumor 1.18188 4.984046 3.296329 0.08432647 0.9381299 4.087467 2.303319 TCGA-BR-8371-01A Tumor 2.8776404 3.757184541 4.087066255 2.124375845 3.02293125 2.470828026 2.022997096 TCGA-KB-A93J-01A Tumor 0.875837139 1.941045437 3.072161717 0.075773007 2.156471938 3.504748286 1.429318621 TCGA-D7-A4YU-01A Tumor 2.063639048 3.259575532 4.4608621 0.218616946 0.924508037 2.823378879 2.04255988 TCGA-BR-6705-01A Tumor 1.038298247 2.900775513 3.64566018 0.49186915 0.951779151 4.168917332 4.161165329 TCGA-BR-6803-01A Tumor 1.879246 2.717687 4.102304 0.4707789 1.231517 3.675672 3.010725 TCGA-D7-A6EX-01A Tumor 6.050786 3.036801 6.044327 2.743125 0.9005351 3.932199 0.6085336 TCGA-HU-A4G9-01A Tumor 0.1595753 5.28807 0.3403798 0.0197615 0.006776058 2.836943 0.8722456 TCGA-BR-6564-01A Tumor 1.496590862 3.029448458 3.894481477 0.26655414 0.275988406 3.363952787 2.834366662 TCGA-D7-A4YX-01A Tumor 1.383958 5.157745 2.550326 0.04208807 0.0423404 3.336927 1.010928 TCGA-CG-4441-01A Tumor 0.5399682 3.240638 3.847987 0.1153327 0.6550857 3.586973 0.8950074 TCGA-VQ-A8DV-01A Tumor 1.942445321 2.004106499 2.02466913 0.949860375 0.035407351 3.511745974 1.115429722 TCGA-CG-5719-01A Tumor 0.58830405 2.81880645 3.242846613 0.285514866 0.64799186 3.688851827 1.425078517 TCGA-HU-A4GX-01A Tumor 1.342377967 2.713753734 4.273368526 0.187861109 0.303005856 2.546742304 0.886186244 TCGA-BR-8483-01A Tumor 1.070246571 3.72921454 3.309582341 0.117455966 0.639095315 2.799359941 0.799753767 TCGA-VQ-A8PC-01A Tumor 0.962254692 3.008823683 3.449828122 0.388967842 0.270040012 3.326448843 1.922492417 TCGA-CD-8526-01A Tumor 2.75320033 1.666904709 3.323253662 4.047264993 2.242766968 3.918581302 2.832770337 TCGA-BR-8380-01A Tumor 2.018217 3.214526 4.721365 0.4832167 1.363491 3.575319 1.83399 TCGA-VQ-A8PQ-01A Tumor 1.415177765 1.85611729 3.521551559 1.701964858 3.135158603 2.841257644 1.608991796 TCGA-BR-8291-01A Tumor 1.184943 2.553363 4.159287 0.9106767 0.1993307 3.624345 2.216754 TCGA-HU-A4GQ-01A Tumor 1.216920374 2.735380858 4.054753957 0.143067313 0.228057516 1.876328585 0.958619388 TCGA-BR-8081-01A Tumor 0.732473344 2.898670394 3.719736897 0.270137247 0.139058075 3.03789501 1.664248393 TCGA-HU-A4H4-01A Tumor 1.586466 1.82869 3.419984 0.06524 0.02197978 3.688176 1.566526 TCGA-VQ-A91K-01A Tumor 0.701677 4.057422 2.851649 0.07834751 0.4482536 3.138717 1.015119 TCGA-R5-A7ZE-01B Tumor 1.211488 2.341332 2.674655 0.0157871 0.03743958 4.755514 0.3228275 TCGA-BR-4367-01A Tumor 1.112890065 2.586554295 3.882900983 0.321071918 0.750927961 3.202550761 1.146288469 TCGA-BR-8297-01A Tumor 2.327849306 2.602756897 4.706686662 0.659324768 1.594581357 2.66196514 2.02751608 TCGA-BR-8687-01A Tumor 0.6432743 4.031101 2.007246 0.3557831 0.7159618 3.36718 1.223462 TCGA-BR-8683-01A Tumor 3.050917169 3.503416035 5.128847446 0.261488514 0.536375552 4.148527523 2.120778249 TCGA-F1-A72C-01A Tumor 0.739025063 2.787533441 4.047641053 0.227383661 0.339662407 3.554120709 1.532078908 TCGA-VQ-A8PM-01A Tumor 0.897091313 3.290353574 3.653633766 1.439687617 1.661737657 3.713296756 2.215429254 TCGA-VQ-A925-01A Tumor 0.6858951 3.953715 3.498419 0.1635345 0.3988967 2.851165 1.424987 TCGA-IN-7808-01A Tumor 1.891662595 1.03730903 2.403261061 2.361808936 0.305003452 2.725390668 1.530478617 TCGA-HU-A4G8-01A Tumor 0.608693755 3.17701403 2.965114114 0.152312149 0.208146993 3.103584164 1.06336513 TCGA-CD-A48A-01A Tumor 0.989641278 2.845248372 2.681126364 0.270661933 1.199705715 2.205555188 0.76140304 TCGA-B7-A5TJ-01A Tumor 0.9022934 3.277641 3.096667 0.03885896 0.1685718 3.291315 1.069075 TCGA-IN-8462-01A Tumor 0.932895484 3.496937542 2.711421183 0.211856053 1.293639808 4.347355311 1.771494371 TCGA-BR-4294-01A Tumor 0.1751223 1.229317 1.119145 0.06609572 1.152652 1.641892 0.8281018 TCGA-BR-A4J4-01A Tumor 2.170208386 4.482231271 4.920350989 0.106800477 0.728821603 3.327186654 0.739869113 TCGA-IN-7806-01A Tumor 0.622760413 3.059874877 3.645457402 0.130679987 0.879915385 3.997686737 2.34787044 TCGA-VQ-AA6F-01A Tumor 0.9762021 3.681372 4.327504 0.1533553 2.933124 3.684511 1.333535 TCGA-BR-A4J8-01A Tumor 1.66036106 3.164610142 3.774383584 0.26047664 0.360689333 3.087742575 1.935377792 TCGA-BR-6707-01A Tumor 0.264970572 2.613814549 1.898067086 0.052691138 1.450594458 3.649117692 1.504507238 TCGA-HU-A4GC-01A Tumor 0.839668959 2.996358274 2.990123012 0.289903447 1.285797217 2.711436741 1.419715995 TCGA-BR-8682-01A Tumor 1.658057 4.011754 4.869761 0.6398398 1.22938 2.991473 2.157898 TCGA-HU-A4H0-01A Tumor 0.1954525 2.097054 2.845189 0.0829983 0.01325216 4.34592 1.299959 TCGA-BR-8677-01A Tumor 2.038649289 3.101007707 3.763084458 0.404288961 0.417569838 3.799483446 3.905616493 TCGA-FP-7998-01A Tumor 1.685827 3.755316 3.249379 0.2442458 0.5586458 4.425912 2.198594 TCGA-D7-8574-01A Tumor 1.064130323 2.346850556 3.712636986 0.726242509 0.365618954 3.010058241 2.212161466 TCGA-VQ-A8P5-01A Tumor 0.811619091 2.816350209 3.847137738 0.447403812 1.230563998 3.253034617 1.265373949 TCGA-CD-8532-01A Tumor 0.759960175 2.185283315 3.461973777 0.319960256 1.235622038 2.885976163 1.382301478 TCGA-VQ-A91A-01A Tumor 1.374345 3.902042 3.207217 0.4994623 0.7897682 3.677264 1.602791 TCGA-CG-4466-01A Tumor 0.597073098 1.293318708 2.572489457 1.572621509 0.67453873 2.064823396 0.323180198 TCGA-BR-8369-01A Tumor 1.814888522 4.004500304 3.703890658 0.30488276 1.170067994 2.732583953 2.599173907 TCGA-D7-A4Z0-01A Tumor 1.490160741 4.179017864 3.755110469 0.562785054 1.214488256 4.588171863 2.247331588 TCGA-CG-4444-01A Tumor 0.835763222 1.417905234 2.540475467 0.218486461 0.803576374 2.173592187 1.406591555 TCGA-BR-7715-01A Tumor 3.593798197 2.168691542 2.106533791 0.338272673 0.21477584 4.106683008 1.489850007 TCGA-BR-8590-01A Tumor 2.301026036 2.678508085 4.371208314 0.867445623 1.405979002 2.753990363 2.18533096 TCGA-VQ-A927-01A Tumor 0.999568385 4.042822443 3.194689296 0.2724281 0.083874399 3.639321449 1.994786183 TCGA-D7-A6EV-01A Tumor 0.3882407 4.827751 3.180008 0.1104833 1.400939 3.614315 1.087342 TCGA-D7-A748-01A Tumor 1.029959683 2.302407569 5.070838698 0.747756573 1.459838371 2.811366495 1.925637951 TCGA-VQ-A91U-01A Tumor 1.009765606 3.765556173 3.927224491 0.083478485 0.166804717 4.207551631 1.412085076 TCGA-IN-8663-01A Tumor 1.634578 4.473471 6.480933 0.0103753 0.1448704 4.668333 0.4830663 TCGA-CG-4477-01A Tumor 1.93565655 2.504399766 2.922328223 0.483535437 0.399406695 4.631779374 1.15662087 TCGA-CG-4460-01A Tumor 0.65891134 2.718746658 2.555019149 1.112653614 0.209293229 2.863646732 1.21087504 TCGA-RD-A8N5-01A Tumor 1.337447623 3.546970365 2.941969508 0.087962696 1.50853324 4.014211571 1.845073681 TCGA-BR-4363-01A Tumor 1.457980389 1.315968685 3.171547866 2.543815192 2.283916304 2.899513704 0.726052769 TCGA-D7-A6EZ-01A Tumor 2.411207 3.895425 2.660239 0.1388036 0.02050613 3.922762 0.3130663 TCGA-IN-A7NT-01A Tumor 2.91324794 1.313807823 6.589516411 0.302031323 1.813989942 3.247854044 0.257589979 TCGA-VQ-A8PD-01A Tumor 1.149639287 3.00054468 2.770045453 0.555181457 0.575945895 3.615866099 2.126211818 TCGA-VQ-A924-01A Tumor 0.434719963 3.417660439 3.669892663 0.026730278 0.058652699 2.833405003 1.001054639 TCGA-IN-A6RN-01A Tumor 1.513373245 4.956728098 3.268909362 0.51606787 0.282539771 3.90230689 1.23104693 TCGA-HU-A4GH-01A Tumor 0.470165863 2.95096698 3.810290694 0.807466826 0.490201716 3.243704581 0.781122483 TCGA-HU-A4H8-01A Tumor 0.2352173 2.511705 2.178387 0.04098654 0.01879883 2.538962 1.39105 TCGA-BR-4370-01A Tumor 2.447075586 2.333969495 4.387745934 0.934489805 0.715475696 2.785908065 1.207813775 TCGA-FP-A9TM-01A Tumor 0.581207 3.356705 3.090762 0.3286333 1.05815 2.49606 1.111386 TCGA-BR-6852-01A Tumor 0.877571057 4.281936328 2.016944797 0.144932013 0.062181197 5.180253982 1.827953374 TCGA-CG-4476-01A Tumor 1.986112067 2.388819272 4.295598374 0.997844941 1.301106034 3.670119893 1.963384057 TCGA-VQ-A8DU-01A Tumor 1.997070671 2.01807414 3.302227944 1.611372423 2.510909456 3.153176815 1.184340778 TCGA-CG-4443-01A Tumor 0.142903267 3.36959046 1.343273298 0.046531971 0.042819101 4.078330331 0.917180166 TCGA-BR-4257-01A Tumor 1.8125 3.284408 2.706983 0.1875158 0.02245521 2.788603 0.9231599 TCGA-D7-6815-01A Tumor 0.627507871 1.999236841 3.975310412 0.101468805 0.050626213 3.660841147 0.833119068 TCGA-BR-A4J9-01A Tumor 2.434034579 2.385616686 5.125573919 0.373723794 0.579740201 2.519146191 2.53061305 TCGA-BR-7723-01A Tumor 0.5481488 3.181986 2.462444 0.3407627 0.03746128 3.611465 3.156063 TCGA-RD-A8NB-01A Tumor 1.813913301 3.685591592 3.977699044 0.178259763 1.021523189 2.906231534 2.030601541 TCGA-D7-6520-01A Tumor 1.688533 1.394036 4.797135 0.04114269 4.378933 3.434748 1.379089 TCGA-BR-6452-01A Tumor 0.578756363 4.252123864 3.265285598 0.097770938 0.670949128 3.121735573 1.382701275 TCGA-IN-A6RR-01A Tumor 0.887838017 4.136092787 3.709633874 0.161197487 1.213619675 3.525163141 1.065288517 TCGA-VQ-A928-01A Tumor 0.834883 3.953051 2.512865 0.06820104 0.1624355 5.845057 1.33201 TCGA-BR-A4J7-01A Tumor 1.886256963 2.836116442 4.612714873 0.179253789 1.863374628 2.211754141 2.238173544 TCGA-BR-8059-01A Tumor 1.130189008 4.798647547 3.149175074 0.133312927 0.441824629 3.339128907 1.078369597 TCGA-VQ-A8DT-01A Tumor 0.485804027 3.749997629 3.213244053 0.18892729 0.113385065 2.791212659 0.675380314 TCGA-VQ-A8P8-01A Tumor 1.443544263 3.708614741 4.107844147 0.901211041 0.702947339 3.241441833 2.215508315 TCGA-VQ-A91D-01A Tumor 0.2015516 3.826989 2.904137 0.1041694 0.002223404 3.411709 0.4139346 TCGA-BR-7901-01A Tumor 1.123011332 3.08818073 3.580712711 0.615076796 1.68760855 4.005573649 2.281382066 TCGA-CG-4306-01A Tumor 1.381822735 3.173588893 3.47874835 0.197974513 0.088026246 2.433389182 0.728868821 TCGA-BR-6565-01A Tumor 0.8861372 1.738328 3.863774 0.8588156 0.2223382 3.466895 1.524099 TCGA-BR-7704-01A Tumor 0.798481387 1.222650643 0.718077766 0.108219421 1.207101961 4.611390083 1.655404944 TCGA-CG-4436-01A Tumor 1.213049 0.8554465 4.137909 0.01771867 0.06543453 4.040544 0.3020501 TCGA-HU-A4G2-01A Tumor 0.5004366 3.350647 2.134837 0.01872161 0.8219181 3.712097 1.065384 TCGA-VQ-A94T-01A Tumor 0.6754407 3.982597 3.506484 0.03453194 0.6601788 4.11358 0.924743 TCGA-VQ-A8PU-01A Tumor 0.5169809 4.583338 3.797617 0.02195526 0.2903077 3.276899 0.8362217 TCGA-VQ-A8PJ-01A Tumor 0.682241791 3.338710447 3.394434759 1.209630114 1.052503612 3.888673555 0.878477261 TCGA-IN-A6RI-01A Tumor 0.1181326 3.829541 0.9077773 0.07880347 1.665936 4.290094 0.8559158 TCGA-IN-A7NU-01A Tumor 0.986536146 5.913750752 4.175180428 0.045420975 0.28278 2.677285689 0.886792567 TCGA-CD-8534-01A Tumor 1.07492996 2.505578695 3.214078508 0.292732212 0.265612513 2.392161054 2.133318765 TCGA-VQ-AA68-01A Tumor 1.222582 3.388123 4.253003 0.08075854 0.8128144 4.726192 1.50404 TCGA-FP-8631-01A Tumor 0.683774921 3.097110492 2.544659798 0.215484799 0.859140967 3.275678327 1.365504973 TCGA-D7-A6EY-01A Tumor 1.43467 3.958112 3.417802 0.1319295 0.6105051 3.902136 1.572472 TCGA-D7-6526-01A Tumor 0.933817416 3.207039171 3.318082097 0.261997425 3.798876318 1.927938896 1.135778264 TCGA-BR-8364-01A Tumor 1.966567674 3.329952948 4.76462949 2.271976199 1.549515921 2.995876183 2.296321149 TCGA-BR-6563-01A Tumor 1.319872 3.162772 3.779765 0.6032088 0.5537031 2.751118 2.858645 TCGA-BR-8676-01A Tumor 0.868585786 1.589702672 4.43459216 0.120233188 0.243753872 1.922788112 0.586986388 TCGA-CG-5721-01A Tumor 2.216479938 0.824726155 3.879840111 0.106681077 0.024812327 3.017940125 1.513742077 TCGA-HF-7133-01A Tumor 3.707496764 5.060224701 3.068940083 0.422492524 0.319458832 3.612241529 1.882421984 TCGA-CD-8528-01A Tumor 0.191428542 2.862391046 2.631908822 0.214166702 0.394083798 2.234906443 0.658095467 TCGA-HU-8244-01A Tumor 0.370961995 2.229410349 2.449515401 0.020204231 0.0360093 4.200920881 0.536067296 TCGA-CD-5813-01A Tumor 1.250586 1.819686 4.128481 0.3170105 0.6794422 3.700488 3.319423 TCGA-BR-8484-01A Tumor 0.619402336 2.625722111 2.331403309 0.260326014 1.75279983 3.693773063 1.676499945 TCGA-BR-6457-01A Tumor 1.561369466 3.102765447 3.965483527 0.404545081 0.850331617 3.319848909 2.52363274 TCGA-FP-7916-01A Tumor 1.040138 4.29032 2.867253 0.2394974 0.366362 3.53875 2.229505 TCGA-BR-4187-01A Tumor 2.375935893 2.55009907 4.693070087 0.36621535 1.161742044 3.018993151 1.370335121 TCGA-KB-A93H-01A Tumor 0.3558624 4.141567 2.344007 0.02343364 0.1309661 2.161633 0.673256 TCGA-BR-8592-01A Tumor 2.370944 2.935553 4.698839 0.9920635 1.692713 3.145616 2.667223 TCGA-BR-4366-01A Tumor 1.368536012 1.89436034 3.679247353 0.36651501 1.240635376 3.806846516 0.920929583 TCGA-BR-7851-01A Tumor 0.7227592 3.67234 3.878413 0.1049021 0.3909773 2.808926 1.527854 TCGA-SW-A7EA-01A Tumor 3.120073 4.317473 3.774933 0.5419694 0.03733677 4.721167 0.3411366 TCGA-CD-5803-01A Tumor 1.520788808 2.65622331 3.867653473 0.17680938 0.766351925 3.500620296 2.687236316 TCGA-D7-6525-01A Tumor 3.780733 3.698342 5.569718 0.1381063 3.022353 2.718937 0.7271086 TCGA-RD-A8N9-01A Tumor 2.059083679 2.627365865 2.757114612 0.895869836 0.931468475 4.101708624 2.170556064 TCGA-BR-4279-01A Tumor 1.266757 1.555858 4.783911 0.8365347 0.8041678 2.128082 1.309666 TCGA-BR-8080-01A Tumor 1.935243589 2.85182438 3.84401359 0.287203492 0.771558627 3.45133926 2.191730731 TCGA-BR-A4PF-01A Tumor 0.559682426 1.460948942 5.007308613 0.009127485 0.008725081 3.358686995 0.896706505 TCGA-HU-A4G3-01A Tumor 0.50014841 4.679153621 1.847138316 0.157006765 0.192734276 3.587090452 1.361639827 TCGA-CD-8531-01A Tumor 0.7905349 0.2333172 0.7912916 0.148216 0.02312529 1.908119 1.07067 TCGA-R5-A7ZF-01A Tumor 2.393267104 2.395231369 3.681226285 1.826620442 1.23166703 3.375924953 0.530415702 TCGA-CD-A487-01A Tumor 1.826746208 4.077834193 3.194445444 0.56315004 0.148626343 2.855645267 1.294507955 TCGA-BR-8384-01A Tumor 2.763102 3.580277 5.196303 0.8444206 1.98113 3.009055 2.761106 TCGA-VQ-A922-01A Tumor 1.035280788 3.197819269 2.785643076 1.173363462 0.607098734 4.542604626 1.975364265 TCGA-B7-A5TI-01A Tumor 0.512300181 2.500331676 3.698463536 0.122988531 0.180678567 3.627176687 1.854537871 TCGA-BR-8368-01A Tumor 0.241820974 2.909913756 4.168378977 0.038593881 1.226194958 3.761766929 1.428094588 TCGA-BR-4357-01A Tumor 0.835714795 2.782859916 2.526174727 0.250874954 0.771976829 2.470444585 1.310104549 TCGA-BR-4371-01A Tumor 1.00235677 2.408807915 3.940115357 0.033870868 0.051192856 3.595726913 0.388713797 TCGA-VQ-A91N-01A Tumor 1.301181 4.104016 3.018144 0.4728672 1.774923 2.946219 0.741594 TCGA-VQ-AA6J-01A Tumor 0.6295464 1.719132 3.8874 0.1254444 0.051952 4.009345 1.552667 TCGA-CG-5724-01A Tumor 2.231384219 2.519507203 5.363975863 0.085708038 0.148396082 2.847123186 0.636341478 TCGA-VQ-A94O-01A Tumor 0.926945262 2.614343031 4.589232297 1.506012748 0.028579469 3.301877502 0.999905309 TCGA-BR-8591-01A Tumor 0.6849949 3.63152 3.741881 0.07964988 0.1906528 4.206365 2.214967 TCGA-VQ-AA64-01A Tumor 1.146117 3.733337 3.667605 0.9597116 0.1090346 4.365559 1.786838 TCGA-FP-8099-01A Tumor 0.845822154 3.799585938 5.364087486 0.094432541 0.377429288 2.603288729 0.736904365 TCGA-F1-A448-01A Tumor 0.6829584 3.824563 2.081768 0.2357484 0.1002473 3.753196 1.96418 TCGA-VQ-A91V-01A Tumor 1.807529 5.142351 3.528629 0.04031713 0.9937077 2.614984 0.9407278 TCGA-RD-A8N0-01A Tumor 1.058342519 3.302072118 4.33710017 1.294795743 0.681841202 3.113228087 2.17949635 TCGA-CD-8525-01A Tumor 0.538279058 2.901421158 2.216583508 0.11439049 0.490875229 3.09609913 1.877687099 TCGA-FP-A4BF-01A Tumor 1.210351272 1.956381685 3.838592914 0.140037589 0.119944237 1.885840645 1.182872928 TCGA-FP-A8CX-01A Tumor 0.3879725 4.171744 3.440068 0.1726682 1.75142 3.383232 1.512573 TCGA-RD-A7BS-01A Tumor 1.63620727 3.19009981 3.42106676 0.71214218 1.0479017 3.98271309 1.30355754 TCGA-BR-7716-01A Tumor 1.385922 3.295404 3.387877 1.031207 0.6938666 3.164252 1.310536 TCGA-BR-8366-01A Tumor 1.329605209 4.608370848 3.785656262 0.305470527 0.530596192 3.816377941 1.880145695 TCGA-VQ-AA6G-01A Tumor 0.3521321 4.796427 4.738453 0.04244572 1.591171 2.896521 1.141117 TCGA-CG-4465-01A Tumor 0.683991979 3.377289485 2.916306603 0.108555034 0.029626471 3.005799273 0.681223595 TCGA-HU-A4H5-01A Tumor 0.5803231 4.216781 2.909884 0.03882796 0.1173441 4.654317 0.9619794 TCGA-CG-4437-01A Tumor 1.503378 1.812456 3.957883 0.1854093 0.7499269 3.3343 1.042541 TCGA-CD-5804-01A Tumor 0.6676371 4.41537 3.014399 0.2783479 2.158988 4.428158 2.305763 TCGA-F1-6875-01A Tumor 2.588222513 5.579199145 2.380100195 1.224212447 2.741433179 5.254255605 1.565317611 TCGA-HF-A5NB-01A Tumor 0.4444563 3.887945 1.2281 0.01991851 0.003988177 4.02035 0.696596 TCGA-BR-8365-01A Tumor 2.311381128 3.284599679 4.637983951 0.793106245 2.26397213 3.213997529 2.502043904 TCGA-CD-8527-01A Tumor 0.598441536 3.22166577 3.143461609 0.193345208 1.838256598 2.117053963 0.739084432 TCGA-D7-A6F0-01A Tumor 0.2823409 3.192723 1.044878 0.3397545 0.05788041 3.180436 1.103288 TCGA-BR-7957-01A Tumor 1.9686025 2.234906101 4.714260202 0.385644658 0.842811581 3.60980803 2.550191273 TCGA-IN-AB1X-01A Tumor 0.4308684 2.952534 6.561791 1.042488 0.297891 3.735652 1.03136 TCGA-BR-8678-01A Tumor 2.936808123 4.632299605 1.347129897 1.985033389 0.322412641 6.169225521 1.347091822 TCGA-D7-6528-01A Tumor 0.259943978 1.076398285 2.014368757 0.053732689 0.063966917 3.266679474 1.492671835 TCGA-HU-8238-01A Tumor 0.539973309 4.217545158 1.783760022 0.216581094 0.186256993 3.359166397 1.401934146 TCGA-BR-8367-01A Tumor 1.733730397 2.218571819 4.061802653 0.497377899 1.18370799 4.025620393 3.477683566 TCGA-BR-7196-01A Tumor 1.557080958 4.05591665 3.210807611 0.786573724 1.125600892 4.154121935 2.99144841 TCGA-FP-7829-01A Tumor 0.861595145 2.322096901 3.195232664 1.12470888 0.574305219 3.661960065 1.546208162 TCGA-B7-A5TN-01A Tumor 0.8008817 3.270453 3.185135 0.1486961 1.010691 3.086995 1.261443 TCGA-VQ-A8E3-01A Tumor 3.081853876 2.324861429 5.311036769 0.092768155 0.178222731 4.309337193 1.337111562 TCGA-CG-5725-01A Tumor 0.4610466 0.9129562 0.9652833 0.7975421 0.5906692 5.552512 2.269484 TCGA-CG-4305-01A Tumor 1.293942682 3.480931833 3.731845157 0.157971372 0.203254544 2.15393282 0.95970696 TCGA-BR-6455-01A Tumor 0.4912628 2.004779 3.168478 0.245262 0.8164237 3.575696 1.79836 TCGA-BR-6802-01A Tumor 2.237238626 4.452667605 3.812924393 0.083782973 0.160953263 3.717150264 1.508182267 TCGA-BR-6709-01A Tumor 1.304852212 2.674542128 5.469953402 0.297723304 0 4.116781791 1.795026969 TCGA-B7-A5TK-01A Tumor 2.790247958 3.519553853 4.212066662 0.39232793 1.184435234 3.565883261 0.760004212 TCGA-CD-A4MH-01A Tumor 1.774527356 1.622508897 4.772584753 0.812929017 0.017353637 1.977078392 1.183384008 TCGA-BR-6710-01A Tumor 0.5014603 3.935222 3.124447 1.085884 1.370884 3.750042 1.164421 TCGA-CD-A4MG-01A Tumor 0.408558629 2.178586719 3.737932171 0.144706044 0.052687207 2.599139911 1.181994138 TCGA-D7-6522-01A Tumor 0.798488815 2.378189553 2.991099653 0.270286941 0.539210361 3.850417526 2.990314693 TCGA-F1-6177-01A Tumor 0.2202665 3.013336 3.940706 0.07485968 0.003056683 2.81519 0.8385951 TCGA-BR-4201-01A Tumor 1.110776878 3.109884788 3.77500545 1.044152598 0.401822683 2.446268874 1.255959157 TCGA-BR-4361-01A Tumor 0.779057622 1.741402136 4.321662528 0.257431201 0.081812558 1.888489023 0.931193544 TCGA-FP-8209-01A Tumor 2.889732937 2.818123064 5.429383674 0.732365581 2.388310001 2.758715616 2.586911179 TCGA-FP-8210-01A Tumor 2.030933 3.10078 4.50584 0.6445545 1.182579 3.603971 3.200544 TCGA-HU-8604-01A Tumor 0.609605188 0.537240551 2.822012706 0.059819904 0.053715488 3.234445189 1.240157146 TCGA-CG-4301-01A Tumor 2.218155132 1.703825126 4.443193429 0.673154255 1.630769396 2.55554707 1.121711676 TCGA-RD-A8N1-01A Tumor 1.309181 3.734235 2.729353 0.6946352 0.1675522 3.652386 1.51391 TCGA-BR-A44U-01A Tumor 0.739773439 0.596297329 4.181761098 0.065296845 0.070783958 2.699349074 0.934189207 TCGA-CG-4469-01A Tumor 0.7742638 2.868779193 3.174743693 0.043350481 0.034632865 2.138822181 0.676936038 TCGA-VQ-A8PH-01A Tumor 0.567102886 1.573253848 2.591524721 1.31473129 0.054552265 3.73145119 1.379976033 TCGA-D7-8576-01A Tumor 0.332246598 4.84088537 2.297837093 0.164890522 0.54804524 3.290941576 1.746987059 TCGA-VQ-AA6K-01A Tumor 1.177972 3.738059 3.807585 0.1387071 2.105817 2.551715 0.9610002 TCGA-HU-8602-01A Tumor 0.2581841 1.520774 1.227869 0.04589277 0.00265045 3.156918 0.6751625 TCGA-BR-8485-01A Tumor 1.115993514 2.905874987 3.479161586 1.012255113 0.266713281 3.209123224 2.096609624 TCGA-VQ-A8E7-01B Tumor 0.6447984 4.328037 4.606298 0.03490118 0.05942971 3.721924 0.8580082 TCGA-HU-A4GJ-01A Tumor 0.834695788 2.582885915 2.105243083 0.885781447 0.315376081 3.010376189 2.047131539 TCGA-BR-8686-01A Tumor 1.158944114 4.594707674 2.072299064 0.666513749 0.859441244 3.846932806 2.550616601 TCGA-BR-8589-01A Tumor 0.299837005 4.46578646 0.777378941 0.072159293 0.124476432 5.430430039 1.084920012 TCGA-RD-A8N6-01A Tumor 1.745753522 2.782853686 4.125771095 1.291744276 1.475206641 2.097827391 1.347060662 TCGA-D7-6524-01A Tumor 1.292202 2.626183 2.994016 0.2596061 0.3947698 3.865072 2.298185 TCGA-CG-5722-01A Tumor 0.708129097 1.912695379 0.983120356 0.448930014 3.991809012 4.042070674 1.80999881 TCGA-BR-8486-01A Tumor 0.773641359 1.757355271 3.445912712 1.457513348 0.021024886 4.337748026 2.08308575 TCGA-VQ-A8PE-01A Tumor 1.060654 3.728101 3.449671 0.5654644 0.06373691 2.722304 1.161948 TCGA-CD-8535-01A Tumor 3.448642876 4.276271395 1.606701787 2.840838724 0.236497622 5.280592404 0.784406031 TCGA-VQ-A91X-01A Tumor 0.359045889 1.41689163 3.070594051 0.457168576 0.057002862 1.454710017 0.087927127 TCGA-BR-A4J5-01A Tumor 2.087054183 3.381186476 4.979104033 0.346152265 0.516752213 3.381307324 2.216084871 TCGA-CD-5798-01A Tumor 1.699647 5.214393 3.643966 0.2980557 1.10999 2.955222 1.320082 TCGA-ZQ-A9CR-01A Tumor 0.622380483 1.562572702 2.702620809 0.17208745 0.406864945 4.176158392 1.368609533 TCGA-D7-6527-01A Tumor 0.685830271 4.377225119 1.914074929 0.117855636 1.354495506 4.442611381 1.933994743 TCGA-BR-8289-01A Tumor 0.7970905 4.1166 2.664657 0.5995189 0.2188737 3.395177 2.245448 TCGA-BR-6801-01A Tumor 1.038954242 2.892986978 3.569035406 0.168670789 0.349912857 4.133195699 1.389112671 TCGA-CG-5734-01A Tumor 0.570689422 3.486578755 2.881354044 0.225528707 0.68820322 3.915146468 1.312834952 TCGA-R5-A805-01A Tumor 0.904367341 3.374181277 3.451089337 0.259143294 2.099891794 4.22670539 1.146024854 TCGA-3M-AB46-01A Tumor 0.929336194 3.034687288 3.440491832 0.038699329 0.638318835 3.410686195 0.847191739 TCGA-CG-5716-01A Tumor 0.468816 4.309629 2.472478 0.2241118 0.5884236 4.172238 1.48064 TCGA-BR-4253-01A Tumor 1.54830758 1.789903524 1.589092939 0.127839018 0.470029011 3.394961479 0.530175828 TCGA-BR-8058-01A Tumor 1.000026 1.919971 2.831898 0.4914572 1.265224 3.235061 2.32879 TCGA-VQ-A8P3-01A Tumor 1.277491098 5.012640985 2.492433597 0.211982331 0.084155239 5.264669824 1.809225156 TCGA-HU-A4H3-01A Tumor 3.259066475 5.068083504 3.72511999 0.063896873 0.059198283 2.945996538 0.956132045 TCGA-BR-4267-01A Tumor 0.419723925 5.002360572 1.544400487 0.042913474 0.063127975 4.661098229 0.804145884 TCGA-VQ-A8E2-01A Tumor 2.180529292 3.166737796 5.129316699 1.817312155 0.351384451 4.386931516 1.883820924 TCGA-MX-A5UG-01A Tumor 1.571898823 2.683611456 3.99258666 1.289054122 0.299388383 4.131193697 2.754382942 TCGA-RD-A8N4-01A Tumor 2.998312461 2.771108635 5.554762791 0.251474006 1.888839452 3.199874985 2.559988876 TCGA-IN-A6RJ-01A Tumor 0.226128517 0.892507644 1.316032256 0.012058536 0.245512202 5.822063898 0.504484659 TCGA-CG-5723-01A Tumor 3.580079 0.7067426 2.098517 0.5937615 0.3726365 2.667186 0.6921303 TCGA-VQ-AA6D-01A Tumor 0.644128773 2.95144263 3.310185935 0.618630161 2.603245488 3.15139191 0.644759971 TCGA-F1-6874-01A Tumor 0.600310017 3.62863408 4.708174875 0.103594363 1.841751492 4.157553869 1.252503129 TCGA-CG-4304-01A Tumor 1.043310125 3.718703321 3.472636511 0.136346451 0.125491852 2.691600726 1.030053443 TCGA-VQ-A923-01A Tumor 0.791169144 4.288717775 3.033498767 0.434594016 0.158728293 4.124312779 2.274151472 TCGA-VQ-A8PF-01A Tumor 0.6814642 3.529904 2.909804 0.1229827 0.3342978 4.561091 2.325173 TCGA-BR-8361-01A Tumor 0.582259393 1.500645105 2.191150455 0.065756039 0.056300031 3.229600864 2.323622601 TCGA-BR-8690-01A Tumor 1.091391477 2.483589445 3.795858334 0.501846744 0.782694464 2.292179431 0.483070808 TCGA-HJ-7597-01A Tumor 0.66829068 3.494525775 5.34984253 0.306765815 0.144536798 2.705735001 0.696418708 TCGA-RD-A7BT-01A Tumor 0.767497553 1.427138138 4.033558011 0.056017273 0.028953851 3.380870786 0.64540714 TCGA-MX-A5UJ-01A Tumor 1.99270593 2.790147673 3.144259148 0.178925791 0.55334595 3.47539643 1.836948663 TCGA-VQ-A91Q-01A Tumor 1.324762039 5.136629207 3.889440936 0.542963671 0.643017773 5.471155507 1.767477882 TCGA-D7-5578-01A Tumor 0.654636 1.388558 2.274012 0.1807723 0.0452988 3.308573 1.554252 TCGA-SW-A7EB-01A Tumor 0.653730759 3.611270752 2.546593943 0.452839824 0.463312472 2.85723383 1.408615166 TCGA-HU-A4GU-01A Tumor 0.2087343 4.18165 4.338861 0.02524666 0.02264258 2.5057 0.4558563 TCGA-D7-6521-01A Tumor 0.785078 2.768624 4.825989 0.4599257 4.324108 4.011548 2.672791 TCGA-IN-AB1V-01A Tumor 1.452058009 3.488256554 2.400881384 0.16487734 1.02692691 5.468461349 0.540523872 TCGA-HF-7134-01A Tumor 0.4566849 1.171188 4.485075 0.03026643 0.006077515 3.789074 0.9651072 TCGA-CD-A48C-01A Tumor 1.065703096 2.598547624 5.034841833 0.502737592 0.868358804 2.502134401 1.043504699 TCGA-HU-8610-01A Tumor 0.9027969 2.550445 1.668782 0.01597307 0.003832795 5.140346 0.9576618 TCGA-BR-8373-01A Tumor 1.053330298 4.112924751 5.044484498 1.426718227 0.229262247 3.843468942 1.715242724 TCGA-EQ-8122-01A Tumor 1.057794938 3.464942161 2.725877117 0.345323448 1.299983216 3.108786863 1.915344455 TCGA-B7-5818-01A Tumor 0.242827964 3.205541196 3.521393564 0.053252019 0.00539077 4.18342121 0.473191056 TCGA-D7-A6F2-01A Tumor 0.739902864 2.18106263 3.774562693 0.092956742 2.039759392 2.649974762 1.181131652 TCGA-RD-A7C1-01A Tumor 0.793228475 3.370873724 1.656217935 0.467553023 0.460650563 3.396348892 1.092408729 TCGA-HF-7131-01A Tumor 0.8002986 3.820362 3.220113 0.1298128 0.6948083 4.424932 1.345389 TCGA-CD-5799-01A Tumor 0.2614236 3.058876 2.898 0.2195201 0.04587698 3.944999 0.8317497 TCGA-VQ-A91S-01A Tumor 0.564048064 2.22221958 3.316148852 1.903319165 0.064633045 2.933151169 0.753028307 TCGA-HU-A4GY-01A Tumor 1.149567403 1.811285782 4.0182157 0.797354233 0.992232692 2.609103395 2.530788394 TCGA-HU-8608-01A Tumor 0.9521978 3.393566 2.490533 0.08182295 0.01723818 5.106018 1.429297 TCGA-CD-A489-01A Tumor 2.131037267 2.685309947 5.065883346 0.408453014 0.831509953 3.21127009 1.896915726 TCGA-BR-6566-01A Tumor 0.47232569 2.751577134 2.174634518 0.057873798 0 3.173049636 0.727161951 TCGA-BR-A4J6-01A Tumor 1.097417 6.463576 3.034636 0.3510019 0.1925431 4.381261 0.9474896 TCGA-BR-8286-01A Tumor 1.413375329 3.499440645 3.41280938 0.185038197 0.390010192 4.812241006 1.744870601 TCGA-CD-8529-01A Tumor 1.044818087 3.660512626 3.118415046 0.410159634 0.490848227 3.961382022 2.697189653
代码：
library(reshape2)
library(ggpubr)
inputFile <- "input.txt" # 输入文件
outFile <- "vioplot.pdf" # 输出文件
setwd("") # 修改工作目录
# 读取文件
rt <- read.table(inputFile, header = T,sep = "\t", check.names = F, row.names = 1)
x <- colnames(rt)[1]
colnames(rt)[1] <- "Type"
# 把数据转换成ggplot2数据文件
data <- melt(rt, id.vars = c("Type")) #将基因表达量根据“Type”进行融化
colnames(data) <- c("Type", "Gene", "Expression")
# 绘制小提琴图
p <- ggviolin(data, x = "Gene", y = "Expression", color = "Type",
ylab = "Gene expression", xlab = x,
legend.title = x,
add.params = list(fill = "white"),
palette = c("blue", "red"),
width = 1,
add = "boxplot")
p <- p + rotate_x_text(60) # 旋转x轴文本60度
p1 <- p + stat_compare_means(aes(group = Type), # 将均值比较 P值添加到 ggplot
method = "wilcox.test",
symnum.args = list(cutpoints = c(0, 0.001, 0.01, 0.05, 1),
symbols = c("***", "**", "*", " ")), # 对P值进行符号数字编码
label = "p.signif") # 显示P值的显著性水平
# 输出
pdf(file = outFile, width = 6, height = 5)
print(p1)
dev.off()
3. 多个基因表达_临床特征分组
输入数据：
id Stage SEMA3A SEMA3B SEMA3C SEMA3D SEMA3E SEMA3F SEMA3G TCGA-F1-6177-01A Stage I 0.2202665 3.013336 3.940706 0.07485968 0.003056683 2.81519 0.8385951 TCGA-IN-A6RI-01A Stage I 0.1181326 3.829541 0.9077773 0.07880347 1.665936 4.290094 0.8559158 TCGA-VQ-A8PX-01A Stage I 0.391461954 4.230095184 1.720071972 0.03215389 0.539633486 3.560325437 0.990870372 TCGA-HU-8610-01A Stage I 0.9027969 2.550445 1.668782 0.01597307 0.003832795 5.140346 0.9576618 TCGA-IN-A6RJ-01A Stage I 0.226128517 0.892507644 1.316032256 0.012058536 0.245512202 5.822063898 0.504484659 TCGA-F1-6875-01A Stage I 2.588222513 5.579199145 2.380100195 1.224212447 2.741433179 5.254255605 1.565317611 TCGA-BR-8486-01A Stage I 0.773641359 1.757355271 3.445912712 1.457513348 0.021024886 4.337748026 2.08308575 TCGA-HU-A4G9-01A Stage I 0.1595753 5.28807 0.3403798 0.0197615 0.006776058 2.836943 0.8722456 TCGA-CG-4443-01A Stage I 0.142903267 3.36959046 1.343273298 0.046531971 0.042819101 4.078330331 0.917180166 TCGA-IN-A6RO-01A Stage I 0.6163783 1.590592 4.669849 0.002290095 1.09423 2.889296 0.4166468 TCGA-IN-A6RS-01A Stage I 0.3461303 0.8250202 2.156692 0.002688006 0.09936001 3.803562 0.6397637 TCGA-CG-5726-01A Stage I 0.1253805 3.138453 1.15533 0.003168569 0.01882528 2.261293 0.6888249 TCGA-IN-AB1V-01A Stage I 0.452058009 3.488256554 2.400881384 0.16487734 1.02692691 5.468461349 0.540523872 TCGA-HU-8244-01A Stage I 0.370961995 2.229410349 2.449515401 0.020204231 0.0360093 4.200920881 0.536067296 TCGA-HF-7134-01A Stage I 0.4566849 1.171188 4.485075 0.03026643 0.006077515 3.789074 0.9651072 TCGA-HU-A4GH-01A Stage I 0.470165863 2.95096698 3.810290694 0.807466826 0.490201716 3.243704581 0.781122483 TCGA-CG-5720-01A Stage I 0.4694241 2.370338 2.524386 0.09574594 0.01679771 3.37344 2.011199 TCGA-KB-A93G-01A Stage I 0.527477971 1.856737647 3.251949066 0.870613018 0.724239271 3.997242724 1.977862955 TCGA-VQ-A8DV-01A Stage I 0.942445321 2.004106499 2.02466913 0.949860375 0.035407351 3.511745974 1.115429722 TCGA-B7-5818-01A 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1.424987 TCGA-VQ-A91Z-01A Stage III 1.464593 4.355924 2.829831 1.366626 0.3527911 5.697085 0.3341439 TCGA-BR-6564-01A Stage III 1.496590862 3.029448458 3.894481477 0.26655414 0.275988406 3.363952787 2.834366662 TCGA-CD-8526-01A Stage III 2.75320033 1.666904709 3.323253662 4.047264993 2.242766968 3.918581302 2.832770337 TCGA-HU-A4H6-01A Stage III 0.481619541 3.039718863 1.493515223 0.21020782 0.061288874 3.745157222 2.055125249 TCGA-VQ-A91K-01A Stage III 0.701677 4.057422 2.851649 0.07834751 0.4482536 3.138717 1.015119 TCGA-D7-6818-01A Stage III 0.6201269 1.121709 2.353106 0.5477714 0.2466362 4.753481 1.704684 TCGA-VQ-A8PU-01A Stage III 0.5169809 4.583338 3.797617 0.02195526 0.2903077 3.276899 0.8362217 TCGA-HU-8249-01A Stage III 1.102356332 0.562543358 4.370634549 0.090980029 0.143505159 3.406393032 1.081255586 TCGA-B7-A5TK-01A Stage III 2.790247958 3.519553853 4.212066662 0.39232793 1.184435234 3.565883261 0.760004212 TCGA-D7-5577-01A Stage III 0.47690858 4.297823133 3.304884099 0.080311232 0.065753996 3.166858468 0.611160518 TCGA-VQ-AA6D-01A Stage III 0.644128773 2.95144263 3.310185935 0.618630161 2.603245488 3.15139191 0.644759971 TCGA-FP-8210-01A Stage III 2.030933 3.10078 4.50584 0.6445545 1.182579 3.603971 3.200544 TCGA-BR-7959-01A Stage III 1.544005 2.800879 4.386488 0.6053695 1.475969 3.221628 2.273923 TCGA-CG-4444-01A Stage III 0.835763222 1.417905234 2.540475467 0.218486461 0.803576374 2.173592187 1.406591555 TCGA-VQ-A8E0-01A Stage III 0.218735056 3.429634421 2.859741135 0.139581713 2.530508501 4.243596026 1.369454984 TCGA-BR-A44U-01A Stage III 0.739773439 0.596297329 4.181761098 0.065296845 0.070783958 2.699349074 0.934189207 TCGA-BR-A4IV-01A Stage III 2.144946 2.966931 5.59729 1.370192 1.847926 2.718832 2.529109 TCGA-BR-8683-01A Stage III 3.050917169 3.503416035 5.128847446 0.261488514 0.536375552 4.148527523 2.120778249 TCGA-D7-A4YU-01A Stage III 2.063639048 3.259575532 4.4608621 0.218616946 0.924508037 2.823378879 2.04255988 TCGA-BR-8677-01A Stage 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0.18892729 0.113385065 2.791212659 0.675380314 TCGA-BR-8369-01A Stage III 1.814888522 4.004500304 3.703890658 0.30488276 1.170067994 2.732583953 2.599173907 TCGA-BR-8077-01A Stage III 0.606516781 1.189708945 2.676699421 0.096495714 0.198126851 3.955756507 1.659799108 TCGA-VQ-A94T-01A Stage III 0.6754407 3.982597 3.506484 0.03453194 0.6601788 4.11358 0.924743 TCGA-BR-8690-01A Stage III 1.091391477 2.483589445 3.795858334 0.501846744 0.782694464 2.292179431 0.483070808 TCGA-BR-7723-01A Stage III 0.5481488 3.181986 2.462444 0.3407627 0.03746128 3.611465 3.156063 TCGA-VQ-A91E-01A Stage III 0.3936808 5.752307 2.79411 0.1851439 0.04271142 4.24143 0.8209434 TCGA-VQ-A91A-01A Stage III 1.374345 3.902042 3.207217 0.4994623 0.7897682 3.677264 1.602791 TCGA-VQ-A8PE-01A Stage III 1.060654 3.728101 3.449671 0.5654644 0.06373691 2.722304 1.161948 TCGA-BR-A4PF-01A Stage III 0.559682426 1.460948942 5.007308613 0.009127485 0.008725081 3.358686995 0.896706505 TCGA-BR-7958-01A Stage III 1.416865472 2.529843541 3.900949919 0.40954048 1.692452296 4.307953235 0.993534243 TCGA-BR-6709-01A Stage III 1.304852212 2.674542128 5.469953402 0.297723304 0 4.116781791 1.795026969 TCGA-BR-8589-01A Stage III 0.299837005 4.46578646 0.777378941 0.072159293 0.124476432 5.430430039 1.084920012 TCGA-VQ-A8PK-01A Stage III 0.948315669 3.640310243 3.935124256 0.786960837 4.766284924 3.689627042 0.725814848 TCGA-D7-8570-01A Stage III 0.545300493 2.744661281 2.684238423 0.107452084 0.203850643 4.26102742 0.974975104 TCGA-3M-AB47-01A Stage III 1.098889176 1.593390687 4.378377339 0.466753154 0.234701274 3.465388485 2.950319564 TCGA-F1-A448-01A Stage III 0.6829584 3.824563 2.081768 0.2357484 0.1002473 3.753196 1.96418 TCGA-VQ-A91X-01A Stage III 0.359045889 1.41689163 3.070594051 0.457168576 0.057002862 1.454710017 0.087927127 TCGA-HU-A4H2-01A Stage III 0.35304878 3.555129947 3.160883973 0.118498064 0.122655655 2.590239112 1.103251755 TCGA-BR-6705-01A Stage III 1.038298247 2.900775513 3.64566018 0.49186915 0.951779151 4.168917332 4.161165329 TCGA-VQ-A8PH-01A Stage III 0.567102886 1.573253848 2.591524721 1.31473129 0.054552265 3.73145119 1.379976033 TCGA-BR-8058-01A Stage III 1.000026 1.919971 2.831898 0.4914572 1.265224 3.235061 2.32879 TCGA-BR-8592-01A Stage III 2.370944 2.935553 4.698839 0.9920635 1.692713 3.145616 2.667223 TCGA-BR-8676-01A Stage III 0.868585786 1.589702672 4.43459216 0.120233188 0.243753872 1.922788112 0.586986388 TCGA-RD-A8N1-01A Stage III 1.309181 3.734235 2.729353 0.6946352 0.1675522 3.652386 1.51391 TCGA-HU-8608-01A Stage III 0.9521978 3.393566 2.490533 0.08182295 0.01723818 5.106018 1.429297 TCGA-R5-A805-01A Stage III 0.904367341 3.374181277 3.451089337 0.259143294 2.099891794 4.22670539 1.146024854 TCGA-BR-A4J8-01A Stage III 1.66036106 3.164610142 3.774383584 0.26047664 0.360689333 3.087742575 1.935377792 TCGA-VQ-A8E2-01A Stage III 2.180529292 3.166737796 5.129316699 1.817312155 0.351384451 4.386931516 1.883820924 TCGA-BR-8686-01A Stage III 1.158944114 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1.476122332 TCGA-HF-A5NB-01A Stage III 0.4444563 3.887945 1.2281 0.01991851 0.003988177 4.02035 0.696596 TCGA-BR-8296-01A Stage III 0.810985036 3.836270275 2.696872141 0.63432361 0.541882377 4.441629059 2.188251342 TCGA-BR-8364-01A Stage III 1.966567674 3.329952948 4.76462949 2.271976199 1.549515921 2.995876183 2.296321149 TCGA-VQ-AA6A-01A Stage III 0.845389025 3.599872118 4.301761883 1.992675001 2.548485832 2.246683346 1.061344727 TCGA-FP-7998-01A Stage III 1.685827 3.755316 3.249379 0.2442458 0.5586458 4.425912 2.198594 TCGA-BR-8687-01A Stage III 0.6432743 4.031101 2.007246 0.3557831 0.7159618 3.36718 1.223462 TCGA-HU-A4GQ-01A Stage III 1.216920374 2.735380858 4.054753957 0.143067313 0.228057516 1.876328585 0.958619388 TCGA-BR-8284-01A Stage III 1.044673975 1.6831893 3.649188289 0.137789976 2.550900258 3.731391849 2.224688548 TCGA-CG-4476-01A Stage III 1.986112067 2.388819272 4.295598374 0.997844941 1.301106034 3.670119893 1.963384057 TCGA-VQ-AA6K-01A Stage III 1.177972 3.738059 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0.234422785 3.750046436 0.701671031 TCGA-CG-5724-01A Stage IV 2.231384219 2.519507203 5.363975863 0.085708038 0.148396082 2.847123186 0.636341478 TCGA-BR-7717-01A Stage IV 0.7319209 1.646986 2.464738 0.1804089 0.3870062 2.93681 1.765642 TCGA-R5-A7ZF-01A Stage IV 2.393267104 2.395231369 3.681226285 1.826620442 1.23166703 3.375924953 0.530415702 TCGA-CG-4301-01A Stage IV 2.218155132 1.703825126 4.443193429 0.673154255 1.630769396 2.55554707 1.121711676 TCGA-CG-5722-01A Stage IV 0.708129097 1.912695379 0.983120356 0.448930014 3.991809012 4.042070674 1.80999881 TCGA-CG-5716-01A Stage IV 0.468816 4.309629 2.472478 0.2241118 0.5884236 4.172238 1.48064 TCGA-VQ-A8PQ-01A Stage IV 1.415177765 1.85611729 3.521551559 1.701964858 3.135158603 2.841257644 1.608991796 TCGA-VQ-A922-01A Stage IV 1.035280788 3.197819269 2.785643076 1.173363462 0.607098734 4.542604626 1.975364265 TCGA-CG-4438-01A Stage IV 2.272986408 2.327628537 2.88348591 1.338690609 0.472171834 1.8378065 0.572066979 TCGA-VQ-A928-01A Stage IV 0.834883 3.953051 2.512865 0.06820104 0.1624355 5.845057 1.33201 TCGA-CG-5719-01A Stage IV 0.58830405 2.81880645 3.242846613 0.285514866 0.64799186 3.688851827 1.425078517 TCGA-VQ-A8E7-01B Stage IV 0.6447984 4.328037 4.606298 0.03490118 0.05942971 3.721924 0.8580082 TCGA-BR-7957-01A Stage IV 1.9686025 2.234906101 4.714260202 0.385644658 0.842811581 3.60980803 2.550191273 TCGA-BR-4368-01A Stage IV 2.805810457 3.039543155 4.030005123 0.673127476 0.808959605 2.103774633 1.796570402 TCGA-CG-5721-01A Stage IV 2.216479938 0.824726155 3.879840111 0.106681077 0.024812327 3.017940125 1.513742077 TCGA-BR-8680-01A Stage IV 1.160640439 3.482876516 4.031267716 0.046598621 0.131717012 2.429506489 0.941816399 TCGA-VQ-A8DZ-01A Stage IV 0.5019263 4.120438 2.570922 0.7100363 0.4869014 3.36606 1.345823 TCGA-CG-4440-01A Stage IV 2.845620371 2.68653978 4.374942085 1.461571258 1.950574065 1.916348673 0.654805911 TCGA-IN-A7NR-01A Stage IV 0.755740942 2.703438686 3.826227798 0.373109823 0.618896675 4.07819948 1.367237757 TCGA-VQ-A8PP-01A Stage IV 1.196001 0.5114453 2.741775 0.2560013 0.1352637 2.819331 0.7891131 TCGA-RD-A7BT-01A Stage IV 0.767497553 1.427138138 4.033558011 0.056017273 0.028953851 3.380870786 0.64540714 TCGA-CG-4460-01A Stage IV 0.65891134 2.718746658 2.555019149 1.112653614 0.209293229 2.863646732 1.21087504 TCGA-VQ-A8PM-01A Stage IV 0.897091313 3.290353574 3.653633766 1.439687617 1.661737657 3.713296756 2.215429254 TCGA-CD-8529-01A Stage IV 1.044818087 3.660512626 3.118415046 0.410159634 0.490848227 3.961382022 2.697189653 TCGA-VQ-A91Q-01A Stage IV 1.324762039 5.136629207 3.889440936 0.542963671 0.643017773 5.471155507 1.767477882 TCGA-CG-4306-01A Stage IV 1.381822735 3.173588893 3.47874835 0.197974513 0.088026246 2.433389182 0.728868821 TCGA-HF-7133-01A Stage IV 3.707496764 5.060224701 3.068940083 0.422492524 0.319458832 3.612241529 1.882421984 TCGA-D7-A748-01A Stage IV 1.029959683 2.302407569 5.070838698 0.747756573 1.459838371 2.811366495 1.925637951 TCGA-CG-4465-01A Stage IV 0.683991979 3.377289485 2.916306603 0.108555034 0.029626471 3.005799273 0.681223595 TCGA-VQ-A8PJ-01A Stage IV 0.682241791 3.338710447 3.394434759 1.209630114 1.052503612 3.888673555 0.878477261 TCGA-CG-4469-01A Stage IV 0.7742638 2.868779193 3.174743693 0.043350481 0.034632865 2.138822181 0.676936038 TCGA-R5-A7ZI-01A Stage IV 0.12340956 2.606398211 0.377489707 0.029645556 0.014243327 3.061041955 0.708972103 TCGA-BR-8289-01A Stage IV 0.7970905 4.1166 2.664657 0.5995189 0.2188737 3.395177 2.245448 TCGA-CG-4462-01A Stage IV 1.44904143 3.55664507 3.393401336 0.525955385 1.565791801 3.343363542 2.072490099
代码：
library(ggplot2)
library(reshape2)
inputFile <- "input.txt" # 输入文件
outFile <- "vioplot.pdf" # 输出文件
setwd("") # 工作目录
# 读取输入文件
rt <- read.table(inputFile, header = T, sep = "\t", check.names = F, row.names = 1)
x <- colnames(rt)[1]
colnames(rt)[1] <- "Type"
#差异分析
geneSig <- c("")
for(gene in colnames(rt)[2:ncol(rt)]){ # 对于每一个基因名，执行下列循环
rt1 <- rt[, c(gene, "Type")] # 将基因表达量列和“Type”列提取出来
colnames(rt1) <- c("expression", "Type")
p <- 1 # 设置一个p值的变量，方便后续调取
if(length(levels(factor(rt1$Type)))>2){ # 如果“Type”列的分组数量超过两个
test <- kruskal.test(expression ~ Type, data = rt1) # 对表达数据根据“Type”分组进行Kruskal-Wallis秩和检验
p <- test$p.value # 提取秩和检验的p值
}else{ # 如果“Type”列的分组数量不超过两个
test <- wilcox.test(expression ~ Type, data = rt1) # 对表达数据根据“Type”分组进行Wilcoxon秩和检验
p <- test$p.value # 提取秩和检验的p值
}
Sig <- ifelse(p<0.001, "***", ifelse(p<0.01, "**", ifelse(p<0.05, "*", ""))) # 将p值转换为符号
geneSig <- c(geneSig, Sig) # 合并所有p值
}
colnames(rt) <- paste0(colnames(rt), geneSig) # 将基因和相应的p值符号放到一起
# 把数据转换成ggplot2输入文件
data <- melt(rt, id.vars = c("Type")) # 将基因表达量根据“Type”进行融化
colnames(data) <- c("Type", "Gene", "Expression")
# 绘制
p1 <- ggplot(data, aes(x = Type, y = Expression, fill = Type)) +
guides(fill = guide_legend(title = x)) + # 为每个刻度设置参考线
labs(x = x, y = "Gene expression") + # 设置x、y轴标签
geom_violin() + # 画小提琴图
geom_boxplot(width = 0.2, position = position_dodge(0.9)) + # 画箱线图，调整箱线图宽度
facet_wrap(~Gene, nrow = 1) + # 分面为一行
theme_bw() + # 设置主题
theme(axis.text.x = element_text(angle = 45, hjust = 1)) # 设置x轴标签的旋转角度和水平对齐
# 输出图片文件
pdf(file = outFile, width = 9, height = 5)
print(p1)
dev.off()
