[R] consolidate three function into one
Ding, Yuan Chun
ycding at coh.org
Mon Jan 15 18:57:13 CET 2018
Hi Richard,
Thank you so much!! I understand the problem now, I assign a name to the "ggsurvplot" object and then add print(fig) at bottom of function definition, now figure gets printed on screen.
Ding
# function to generate RFS curves
RFS <- function( inputfile, N ) {
cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
data = inputfile)
if( N==2) {palette <- c("red", "black")
legend.labs <- c("Cluster1", "Cluster2")
}
else if(N==3) {palette <- c("red", "black", "green")
legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
}
else {palette <- c("red", "black","green", "blue")
legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
}
fig <-ggsurvplot(cluster, data = inputfile, risk.table = F,
palette = palette,
ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
main = "Survival curve",pval = TRUE,font.x = 16,font.y = 16,
font.tickslab = 14,font.legend =c(14,"plain","black"),
legend = "bottom",
legend.title = "Tree Cluster",
legend.labs = legend.labs,
lty=1, lwd=3)
print(fig)
}
-----Original Message-----
From: Richard M. Heiberger [mailto:rmh at temple.edu]
Sent: Sunday, January 14, 2018 1:34 PM
To: Ding, Yuan Chun <ycding at coh.org>
Cc: Bert Gunter <bgunter.4567 at gmail.com>; r-help at r-project.org
Subject: Re: [R] consolidate three function into one
FAQ 7.22
You must print a ggplot object, for example with
print(m52.2cluster)
For the FAQ, run the line
system.file("../../doc/FAQ")
in R on your computer.
Open up the resulting filepath in your favorite editor and scroll down to 7.22
On Sun, Jan 14, 2018 at 4:21 PM, Ding, Yuan Chun <ycding at coh.org> wrote:
> Hi Bert,
>
> I am sorry to bother you on weekend.
>
> I am still struggling on defining a correct function.
>
> I first defined the function RFS (see below), then run it by provide the two argument.
>
> m52.2cluster <-RFS(inputfile =allinfo_m52, N=2 )
>
> I do not get error message, but no figure displays on screen. I do not know what is going on.
>
> Can you help me a little more on this issue?
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS <- function( inputfile, N ) {
> cluster<- survfit(Surv(RFS_days2, OV_Had_a_Recurrence_CODE) ~ clusters,
> data = inputfile)
>
> if( N==2) {palette <- c("red", "black")
> legend.labs <- c("Cluster1", "Cluster2")
> }
>
> else if(N==3) {palette <- c("red", "black", "green")
> legend.labs <- c("Cluster1", "Cluster2", "Cluster3")
> }
>
> else {palette <- c("red", "black","green", "blue")
> legend.labs <- c("Cluster1", "Cluster2", "Cluster3", "Cluster4")
> }
>
> ggsurvplot(cluster, data = inputfile, risk.table = F,
> palette = palette,
> ylim=c(0,1),ggtheme = theme_bw(),xlab="Relapse Free Suvival (Days)",
> main = "Survival curve",pval = TRUE,font.x = 16,font.y = 16,
> font.tickslab = 14,font.legend =c(14,"plain","black"),
> legend = "bottom",
> legend.title = "Tree Cluster",
> legend.labs = legend.labs,
> lty=1, lwd=3)
> }
>
> From: Bert Gunter [mailto:bgunter.4567 at gmail.com]
> Sent: Sunday, January 14, 2018 9:50 AM
> To: Ding, Yuan Chun <ycding at coh.org>
> Subject: Re: [R] consolidate three function into one
>
> I have not looked at your code *at all*, so I am not sure what exactly you mean by "consolidate."
> Is this what you are after?
>
> f1 <- function(...) { code 1}
> f2 <- function(...) { code 2}
> f3 <- function(...) { code 3}
> ## can be "consolidated as":
> f <- function( someargs, ...){
> if( expr(someargs)) f1(...)
> else if(expr2(someargs)) f2(...)
> else f3(...)
> }
> The "..." argument to f can soak up any named additional arguments you wish to pass to f1, f2, or f3.
> My apologies if this is offbase or too vague, and feel free to ignore in that case. I don't have the patience to go trough your code in detail. Others may and give you what you want.
> Cheers,
> Bert
>
>
>
> Bert Gunter
>
> "The trouble with having an open mind is that people keep coming along and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
>
> On Sun, Jan 14, 2018 at 9:17 AM, Ding, Yuan Chun <ycding at coh.org<mailto:ycding at coh.org>> wrote:
> HI R users,
>
> I construct dendrogram tree and cut the tree into different clusters, then generate survival curves by the following three functions. All variables are included in an inputfile.
>
> Can you help me to consolidate the following three function into one functions? I thought about using if else function, but not sure how to do it.
>
> Thank you,
>
> Ding
>
> # function to generate RFS
> RFS2cluster <- function( inputfile ) {
> cluster2<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> data = inputfile)
>
> ggsurvplot(cluster2, data = inputfile, risk.table = F,
> palette = c("red", "black"),
> ylim=c(0,1),
> ggtheme = theme_bw(),
> xlab="Relapse Free Suvival (Days)",
> main = "Survival curve",
> pval = TRUE,
> font.x = 16,
> font.y = 16,
> font.tickslab = 14,
> font.legend =c(14,"plain","black"),
> legend = "bottom",
> legend.title = "Tree Cluster",
> legend.labs = c("Cluster1", "Cluster2"), lty=1, lwd=3) }
>
> RFS3cluster <- function( inputfile ) {
> cluster3<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> data = inputfile)
>
> ggsurvplot(cluster3, data = inputfile, risk.table = F,
> palette = c("red", "black", "green"),
> ylim=c(0,1),
> ggtheme = theme_bw(),
> xlab="Relapse Free Suvival (Days)",
> main = "Survival curve",
> pval = TRUE,
> font.x = 16,
> font.y = 16,
> font.tickslab = 14,
> font.legend =c(14,"plain","black"),
> legend = "bottom",
> legend.title = "Tree Cluster",
> legend.labs = c("Cluster1", "Cluster2", "Cluster3"),
> lty=1, lwd=3) }
>
> RFS4cluster <- function( inputfile ) {
> cluster4<- survfit(Surv(RFS_days, OV_Had_a_Recurrence_CODE) ~ clusters,
> data = inputfile)
>
> ggsurvplot(cluster4, data = inputfile, risk.table = F,
> palette = c("red", "black", "green", "blue"),
> ylim=c(0,1),
> ggtheme = theme_bw(),
> xlab="Relapse Free Suvival (Days)",
> main = "Survival curve",
> pval = TRUE,
> font.x = 16,
> font.y = 16,
> font.tickslab = 14,
> font.legend =c(14,"plain","black"),
> legend = "bottom",
> legend.title = "Tree Cluster",
> legend.labs = c("Cluster1", "Cluster2", "Cluster3",
> "Cluster4"), lty=1, lwd=3) }
>
> -----Original Message-----
> From: R-help
> [mailto:r-help-bounces at r-project.org<mailto:r-help-bounces at r-project.o
> rg>] On Behalf Of imane hajar
> Sent: Friday, January 12, 2018 7:42 AM
> To: r-help at r-project.org<mailto:r-help at r-project.org>
> Subject: [R] Help with packages (methods, stats, stats4)
>
> [Attention: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected
> emails.]
>
>
>
>
>
> hello,
> Can you please give me a hand with this problem,well i can't install
> these
> packages:
> - stats
> - methods
> - stats4
>
> when i tried the following command : *library(help = "stats") * , it gave me this output (*see picture*), so i contacted the Maintainer of the package at (*R-core at r-project.org<mailto:R-core at r-project.org> <R-core at r-project.org<mailto:R-core at r-project.org>>*) but he said that i write to the wrong place.
>
> (i want to install those packages in order to use the "DVstats"
> package)
>
> (i have the latest version of R (3.4.3 ) and Rstudio(1.2.240) )
>
> thank you
> Regards
>
>
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