plot_circle: Circular plot using circlize package
In SubgrPlots: Graphical Displays for Subgroup Analysis in Clinical Trials

View source: R/26-circular-plot-function.r

This function produces a circular plot for subgroup analysis using the circlize package. Overlaps across all variable levels are displayed in a single diagram.

plot_circle(
  dat,
  covari.sel,
  trt.sel,
  resp.sel,
  outcome.type,
  range.v = NULL,
  adj.ann.subgrp = 4,
  range.strip = c(-3, 3),
  n.brk = 31,
  n.brk.axis = NULL,
  font.size = c(1, 1, 0.85, 0.85, 1),
  title = NULL,
  lab.xy = NULL,
  strip = "Treatment effect size",
  effect = "HR",
  equal.width = TRUE,
  show.KM = FALSE,
  show.effect = TRUE,
  conf.int = TRUE,
  show.overall = TRUE,
  palette = "divergent",
  col.power = 0.5
)

`dat`	a data set
`covari.sel`	a vector of indices of the two covariates
`trt.sel`	a covariate index specifying the treatment code
`resp.sel`	a covariate index specifying the response variable
`outcome.type`	a string specifying the type of the response variable, it can be "continuous", or "binary" or "survival".
`range.v`	a vector specifying the vertical range of graphical display.
`adj.ann.subgrp`	a parameter adjusting the distance between a point and its corresponding subgroup label. The smaller the value is, the larger the distance is.
`range.strip`	a vector with two elements specifying the range of treatment effect size for display
`n.brk`	a number specifying the number of the points dividing the range of the argument "range.strip".
`n.brk.axis`	a number specifying the number of breakpoints dividing the axis of the argument "range.strip".
`font.size`	a vector specifying the size of labels and text; the first element is for the main title, the second is for for x-axis and y-axis labels; the thrid is for the legend text of subgroups; the fourth is for the subgroup labels near points; the fifth is for the unit labels on all the axes.
`title`	a string specifying the main title.
`lab.xy`	a list of two strings specifying the labels of the x and y axes.
`strip`	a string specifying the title of the colour strip.
`effect`	either "HR" or "RMST". only when outcome.type = "survival"
`equal.width`	A logical indicating whether the sectors should have equal width or proportional to their sample sizes
`show.KM`	A logical indicating whether to show the Kaplan-Meier curves for the subgroups
`show.effect`	A logical indicating whether to show the treatment effect
`conf.int`	A logical indicating whether to show confidence intervals for the treatment effect.
`show.overall`	A logical indicating whether to show the overall treatment effect and its confidence intervals in the reference strip
`palette`	either "divergent" or "hcl"
`col.power`	to be used when palette = "hcl". see colorspace package for reference

library(dplyr)

# Load the data to be used
data(prca)
dat <- prca
vars = data.frame(variable = names(dat), index = 1:length(names(dat)))
levels(dat$age_group) = c("Young","Middle-aged","Old")
levels(dat$weight_group)  = c("Low","Mid","High")
dat %>%
  rename(Age= age_group,
         Weight = weight_group)-> dat

set.seed(55643)
plot_circle(dat,
            covari.sel = c(14, 15),
            trt.sel = 3,
            resp.sel = c(1, 2),
            outcome.type = "survival",
            range.v = NULL, adj.ann.subgrp = 4,
            range.strip=c(-3, 3),
            n.brk = 31,
            n.brk.axis = 7,
            font.size = c(1, 1, 0.85, 0.85, 1),
            title = NULL, lab.xy = NULL,
            strip = "Treatment effect size (log hazard ratio)",
            effect = "HR",
            equal.width = FALSE,
            show.KM = FALSE,
            show.effect = TRUE,
            conf.int = FALSE, palette = "hcl")