Plot seperate Schoenfeld plots for different clusters/subtypes
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omarrafiqued ▴ 50
@omarrafiqued-21833
Last seen 4 months ago
India

I am working in R . I have a gene expression matrix with 100 patients and 10000 genes. I do some clustering analysis on patients and obtain different different groups of patients. 5 clusters are obtained and each patient is allotted a number 1,2,3,4 or 5 depending on which cluster the patient belongs. I also have clinical data frame in R of all the 100 patients in the gene expression matrix. The clinical data contains survival time in days, if death occurred or not (0 or 1). I then combine clinical data and the clustering information and the new data frame looks like :

$ Survival: int 1614 370 183 310 691 1560 268 515 821 537 ...

$ Death : int 1 1 1 1 1 1 1 1 1 1 ...

$ Cluster : int 1 2 2 2 1 1 3 1 4 5 1 ...

I want to plot Schoenfeld plots for each cluster. That means I want 5 Schoenfeld plots.

I use the following code to do it:

fitcox <- coxph(Surv(Survival,Death) ~ as.factor(cluster), data = dataX)

summary(fitcox)

ftest <- cox.zph(fitcox)

ftest

ggcoxzph(ftest)

The problem is that I get only one Schoenfeld plot, instead of multiple plots ( one for each cluster) in the R plots tab.

I would be grateful if someone rectifies this code to obtain the plots for each cluster. There are five clusters. If one cluster is taken as reference then 4 plots are expected.

Thanks.

R survival analysis • 575 views
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