[R] consolidate three function into one
Ding, Yuan Chun
ycding at coh.org
Mon Jan 15 19:21:37 CET 2018
Thank you, your suggestion is simpler and logically better. I had impression that the last object in a function gets returned, so I did not add the print function at the bottom line of the function definition. Returning an object and graph the object are different process, I am a beginner for writing R function and need to find a good guide source about writing R functions. If you know a good book or website for guidance of R function, please let me know.
Thanks,
Ding
From: Bert Gunter [mailto:bgunter.4567 at gmail.com]
Sent: Monday, January 15, 2018 10:11 AM
To: Ding, Yuan Chun <ycding at coh.org>
Cc: Richard M. Heiberger <rmh at temple.edu>; r-help at r-project.org
Subject: Re: [R] consolidate three function into one
That is certainly OK, but you can also just use
print(ggsurvplot(...))
as your final statement.
out <- RFS( ...)
would then return the ggsurvplot object *and* graph it.
Any good R tutorial or a web search will provide more details on function returns, which you might find useful.
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 Mon, Jan 15, 2018 at 9:57 AM, Ding, Yuan Chun <ycding at coh.org<mailto:ycding at coh.org>> wrote:
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<mailto:rmh at temple.edu>]
Sent: Sunday, January 14, 2018 1:34 PM
To: Ding, Yuan Chun <ycding at coh.org<mailto:ycding at coh.org>>
Cc: Bert Gunter <bgunter.4567 at gmail.com<mailto:bgunter.4567 at gmail.com>>; r-help at r-project.org<mailto: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<mailto: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<mailto:bgunter.4567 at gmail.com>]
> Sent: Sunday, January 14, 2018 9:50 AM
> To: Ding, Yuan Chun <ycding at coh.org<mailto: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><mailto: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.org><mailto:r-help-bounces at r-project.o<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><mailto: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><mailto: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><mailto: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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