getCoxPie: Get pie plot of Cox chisq proportion for variants in Cox...

In huangwb8/luckyExperiment: useful functions for biology experiment

Get pie plot of Cox chisq proportion for variants in Cox regression model

Description

Get pie plot of Cox chisq proportion for variants in Cox regression model

Usage

getCoxPie(
  data,
  time.col = "time",
  status.col = "event",
  clusters,
  time.raw.type = c("Day", "Month", "Year")[1],
  time.target.type = c("Day", "Month", "Year")[3],
  global = T,
  pie.color,
  Others.color = mycolor[27],
  pie.label,
  dc = 1,
  legend.name = "Variable",
  legend.position = "right",
  is.title = T,
  plot.size = 7,
  names = "project"
)

Arguments

data	a data frame with survival data(time & event)
time.col	colname of time value
status.col	Numeric.status.col must be a binary parameter with 0(event not happened yet) or 1(event happened) value.
clusters	list of characters.Some of the colnames of the data representing the value involving the glm model.
time.raw.type	one of "Day","Month","Year"
time.target.type	one of "Day","Month","Year"
global	should a global chi-square test be done, in addition to the per-variable or per-term tests tests.
pie.color	a character vector with color value and variable names. Default is missing.
Others.color	the color of others. It works when global=T
dc	the digit counts of proportion
legend.name	the name of legened
legend.position	the position of legend
is.title	whether plot title
plot.size	the size of saved plots
names	part of save files or plots.

Value

pie data and plots

Author(s)

Weibin Huang<[e-mail]>

See Also

cox.zph; cox.ph

Examples

data("myeloma",package = "survminer");
data <- myeloma;rm(myeloma)
show.color(mycolor)
pie.color <- c(TP53="#FB8072", WHSC1="#BEBADA", DEPDC1="#80B1D3", Others="#A65628")
pie.label = c("TP53" = "tp53","WHSC1" = "whsc1","DEPDC1"="depdc1")
a <- getCoxPie(data,
               time.col = "time",
               status.col = "event",
               clusters = list(c("TP53","WHSC1"),
                               c("TP53","WHSC1","DEPDC1")),
               time.raw.type = c("Day", "Month","Year")[2],
               time.target.type = c("Day", "Month", "Year")[3],
               global=T,
               pie.color = pie.color,
               pie.label = pie.label,
               plot.size = 7,
               names = "project")

huangwb8/luckyExperiment documentation built on June 29, 2023, 10:15 a.m.