compareTreatmentPlans: Compare and Draw the KM curve of specified treatment plan or...

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

Compare and Draw the KM curve of specified treatment plan or exposure in selected nodes

Description

Based on the survival tree, specify the node of interest and the treatment methods, draw survival curves to evaluate the impact of treatments or exposure.

Usage

compareTreatmentPlans(
df,
treepoints,
mytree,
source,
treatment
)

Arguments

df	"data" in the return result of the survivalpath() function
treepoints	list object;Specify the node for drawing the KM curve, which is displayed in the survival path graphs
mytree	"tree" in the return result of the survivalpath() function
source	Data.frame of time slice data, which could be returned by timedivision()
treatment	Factor variable in the source data.frame. This argument is to specify the intervention or exposure that of interest at a specific node.

Details

The function creates survival curves of specified treatment plan or exposure in selected nodes. The results should be interpreted with caution as the effect of covariates have not been adjusted.

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))

#Comparing the efficacy of treatment methods by drawing survival curves
treepoints = c(14,20)
compareTreatmentPlans(result$data, treepoints,mytree,dataset,"Resection")

SurvivalPath documentation built on July 4, 2022, 1:05 a.m.