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p-value is not visible on jskm() plot... #7

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IMCPatrick opened this issue Oct 22, 2023 · 24 comments
Closed

p-value is not visible on jskm() plot... #7

IMCPatrick opened this issue Oct 22, 2023 · 24 comments

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@IMCPatrick
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IMCPatrick commented Oct 22, 2023 •
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AllDeathKM <- survfit(data = psBB, Surv(All_Mortality_3yr_Duration, All_Mortality_3yr) ~ BB_DC)
jskm(AllDeathKM,
cumhaz = T, surv.scale = "percent", marks = F, showpercent = T, ci = F,
pval = T, pval.testname = F, pval.coord = c(0.2,0.2), pval.size = 5,
main = "All cause mortality",
ystrataname = "Beta Blocker", ystratalabs = c("BB(+)","BB(-)"),
ylabs = "Cumulative Incidence", ylims = c(0, 0.075),
xlabs = "Time(Day)", xlims = c(0,1100),
legend = T, legendposition = c(0.85, 0.9),
table = T, size.label.nrisk = 8, label.nrisk = "No. at Risk",
timeby = 150, cut.landmark = 30)

as shown above, I typed 'pval = T' definitely. But after Ctrl + Enter, There's no p-value on K-M plot.
I re-installed package(jskm), nothing's changed.
What should I do to display p-value on my landmark analysis K-M plot???

위 코드대로 입력하면, pval = T를 입력했는데도 p-value가 plot 위에 표시되지 않습니다...
버전의 문제인가 싶어 R 및 Package도 재설치 해봤지만 해결되지 않습니다....ㅠ
하지만 인터넷의 예제를 그대로 따라하면 p-value가 나타납니다.
데이터셋 자체의 무엇을 수정해야 하는 문제일까요?
@jinseob2kim
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ylims와 pval.coord를 조절해보셨을지요? 디폴트 옵션일때도 안나오는지 확인부탁드립니다

@IMCPatrick
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IMCPatrick commented Nov 4, 2023 via email

@jinseob2kim
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Landmark 옵션 제외해도 안보이시는지요? Landmark에서 p를 두개 보여주는 과정에서 화면에 걸릴수 있습니다

@jinseob2kim
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Ylims 의 0.075를 pval.coord 의 0.2보다 크게 한번 부탁드립니다. Pvalue 위치는 아래처럼 지정됩니다

 p <- p + annotate("text", x = c(pval.coord[1], pval.coord[1] + cut.landmark), y = pval.coord[2], label = pvaltxt, size = pval.size)

@IMCPatrick
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IMCPatrick commented Nov 4, 2023 via email

@jinseob2kim
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pval.coord =(10, 0.075) 로 해보시겠어요. 그래도 안되신다면 데이터를 [email protected]로 보내주시면 확인해보겠습니다

@IMCPatrick
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IMCPatrick commented Nov 4, 2023 via email

@jinseob2kim
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제가 실행해보니 P가 나오긴하는데, lanmark가 30일로 짧아 값이 겹치게 나옵니다.

  • PPT로 저장하신 후 직접 편집하실 수 있습니다.
  • 아래는 코드이고, 다운받은 PPT에서 P값 제가 위치 바꾼 파일을 메일로 첨부드립니다.
library(survival);library(jskm)
psBB <- read.csv("BB_3yr_Final.csv")

AllDeathKM <- survfit(data = psBB, Surv(All_Mortality_3yr_Duration, All_Mortality_3yr) ~ BB_DC)
summary(AllDeathKM, times = c(30, 1100), extend = T)
res.km <- jskm(AllDeathKM,
               cumhaz = T, surv.scale = "percent", marks = F, showpercent = T, ci = F,
               pval = T, pval.testname = F, pval.coord = c(10,0.075), pval.size = 5,
               main = "All cause mortality",
               ystrataname = "Beta Blocker", ystratalabs = c("BB(+)","BB(-)"),
               ylabs = "Cumulative Incidence", ylims = c(0, 0.1),
               xlabs = "Time(Day)", xlims = c(0,1100),
               legend = T, legendposition = c(0.85, 0.9),
               table = T, size.label.nrisk = 8, label.nrisk = "No. at Risk",
               timeby = 150, cut.landmark = 30)


## Save to PPTx
library(officer);library(rvg);library(magrittr)
doc <- read_pptx() %>% 
  add_slide("Title and Content", "Office Theme") %>% 
  ph_with(dml(ggobj = res.km), location = ph_location(width = 10, height = 6))

print(doc, target = "km.pptx")

@IMCPatrick
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IMCPatrick commented Nov 5, 2023 via email

@jinseob2kim
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저장한 PPT를 파워포인트에서 여신 후, 마우스 드래그하시면됩니다.
-p 뿐만 아니라 선 색깔부터 글씨폰트 및 크기까지 전부 수정가능합니다.

@IMCPatrick
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IMCPatrick commented Nov 7, 2023 via email

@jinseob2kim
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그림그리셨던 코드 옵션 알려주시면 확인하겠습니다

@IMCPatrick
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IMCPatrick commented Nov 8, 2023 via email

@jinseob2kim jinseob2kim reopened this Nov 9, 2023
@jinseob2kim
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늦어서 죄송합니다. 이전에 알려드린 아래코드로 저장했는데 P값이 나옵니다. 아래코드로 만든 ppt 첨부드립니다.

  • 겹쳐서 나와서 분리하면 됩니다.
    km (1).pptx
## Save to PPTx
library(officer);library(rvg);library(magrittr)
doc <- read_pptx() %>% 
  add_slide("Title and Content", "Office Theme") %>% 
  ph_with(dml(ggobj = res.km), location = ph_location(width = 10, height = 6))

print(doc, target = "km.pptx")

@IMCPatrick
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IMCPatrick commented Nov 19, 2023 via email

@jinseob2kim
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위의 제가 첨부드린 PPT에선 p값이 보이실지요? 그렇다면 직접 만드신 PPT 파일 첨부부탁드립니다

@IMCPatrick
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IMCPatrick commented Nov 19, 2023 via email

@jinseob2kim
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PPT 파일 첨부부탁드립니다

@IMCPatrick
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IMCPatrick commented Nov 19, 2023 via email

@jinseob2kim
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jinseob2kim commented Nov 19, 2023 •
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선생님께. [email protected] 로 바로 보내주시면 감사하겠습니다

@IMCPatrick
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IMCPatrick commented Nov 19, 2023 via email

@IMCPatrick
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IMCPatrick commented Nov 19, 2023 via email

@jinseob2kim
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혹시 All_Mortality_3yr 변수도 factor로 바꾸셨을지요? 그렇다면 survfit을 아래처럼 바꿔야합니다.

AllDeathKM <- survfit(data = psBB, Surv(All_Mortality_3yr_Duration, All_Mortality_3yr == 1) ~ BB_DC)

@IMCPatrick
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IMCPatrick commented Nov 19, 2023 via email

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@jinseob2kim @IMCPatrick