plotKM: Compare and Draw the KM curves of any given nodes

In zhangt369/SurvivalPath: Construction and Visualization of Survival Path Tree using Time-Series Survival Data

Compare and Draw the KM curves of any given nodes

Description

According to the survival path tree, draw the KM curves of the using any nodes on the survival tree

Usage

plotKM(
df,
treepoints,
mytree,
risk.table=TRUE
)

Arguments

df	"data" in the returned result of the survivalpath() function
treepoints	list object;Specify the node for drawing the KM curve, which is in the survival path tree
mytree	"tree" in the returned result of the survivalpath() function
risk.table	Logical value. Allowed values include:TRUE or FALSE specifying whether to show the risk table. Default is FALSE.

Details

Plot survival curves for patients contained in nodes in the survival path tree.

Value

No return value.

See Also

survminer

Examples

library(dplyr)
data("DTSDHCC")
id = DTSDHCC$ID[!duplicated(DTSDHCC$ID)]
set.seed(123)
id = sample(id,500)
miniDTSDHCC <- DTSDHCC[DTSDHCC$ID %in% id,]
dataset = timedivision(miniDTSDHCC,"ID","Date",period = 90,left_interval = 0.5,right_interval=0.5)
resu <- generatorDTSD(dataset,periodindex="time_slice",IDindex="ID" ,timeindex="OStime_day",
 statusindex="Status_of_death",variable =c( "Age", "Amount.of.Hepatic.Lesions",
 "Largest.Diameter.of.Hepatic.Lesions",
 "New.Lesion","Vascular.Invasion" ,"Local.Lymph.Node.Metastasis",
 "Distant.Metastasis" , "Child_pugh_score" ,"AFP"),predict.time=365*1)
result <- survivalpath(resu,time_slices =9)

mytree <- result$tree

library(ggplot2)
library(ggtree)
ggtree(mytree, color="black",linetype=1,size=1.2,ladderize = TRUE )+
 theme_tree2() +
 geom_text2(aes(label=label),hjust=0.6, vjust=-0.6 ,size=3.0)+
 geom_text2(aes(label=paste(node,size,mytree@data$survival,mytree@data$survivalrate,sep = "/")),
 hjust=0.6, vjust=-1.85 ,size=3.0)+
 #geom_point2(aes(shape=isTip, color=isTip), size=mytree1@data$os/40)+
 geom_point2(aes(shape=isTip, color=isTip), size=mytree@data$size%/%200+1,show.legend=FALSE)+
 #guides(color=guide_legend(title="node name/sample number/Median survival time/Survival rate")) +
 labs(size= "Nitrogen",
      x = "TimePoints",
      y = "Survival",
      subtitle = "node_name/sample number/Median survival time/Survival rate",
      title = "Survival Tree") +
 theme(legend.title=element_blank(),legend.position = c(0.1,0.9))

#plot KM curve
treepoints = c(14,20)
plotKM(result$data, treepoints,mytree,risk.table=T)

zhangt369/SurvivalPath documentation built on Jan. 31, 2023, 1:57 a.m.