plot_mosaic: Mosaic plot

In SubgrPlots: Graphical Displays for Subgroup Analysis in Clinical Trials

Description

This function produces a mosaic plot for subgroup analysis

Usage

plot_mosaic(
  dat,
  covari.sel,
  trt.sel,
  resp.sel,
  outcome.type,
  range.v = NULL,
  adj.ann.subgrp = 4,
  range.strip = c(-3, 3),
  n.brk = 30,
  n.brk.axis = NULL,
  font.size = c(1, 1, 0.85, 0.85, 1),
  title = NULL,
  lab.xy = NULL,
  strip = "default",
  effect = "HR",
  lwd. = 2,
  sep. = 0.05,
  show.overall = TRUE,
  palette = "divergent",
  col.power = 0.5,
  print.ss = FALSE,
  col.line = "white",
  time = NULL,
  show.marginal = TRUE,
  show.effect = TRUE,
  grid.newpage = TRUE
)

Arguments

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	range for the treatment effect scale
n.brk	number of breaks in the treatment effect scale
n.brk.axis	number of breaks in the axis of the treatment effect scale
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 third 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	title for the treatment effect scale
effect	either "HR" or "RMST". only when outcome.type = "survival"
lwd.	line width for the mosaics
sep.	separation for the mosaics
show.overall	logical. whether to show or not the overall treatment effect in the strip
palette	either "divergent" or "hcl"
col.power	to be used when palette = "hcl". see colorspace package for reference
print.ss	logival indicating whether to show the sample sizes of subgroups
col.line	color of the mosaics' border
time	time for calculating the RMST
show.marginal	logical indicating whether to show the marginal subgroups. only when 2 covariates are used
show.effect	logical indicating whether to show effect size using color or not. only when 3 covariates are used
grid.newpage	logical. If TRUE (default), the function calls grid::grid.newpage() to start from an empty page.

Examples

library(dplyr)
data(prca)
dat <- prca
dat %>%
  mutate(bm = factor(ifelse(bm == 0 , "No", "Yes")),
         hx = factor(ifelse(hx == 0 , "No", "Yes")),
         Treatment = factor(ifelse(rx == 0 , "Control", "Treatment")),
         Survival = factor(ifelse(survtime > 24 , "Yes", "No"),
         levels = c("Yes", "No")))-> dat
levels(dat$age_group) = c("Young","Middle-aged","Old")
levels(dat$weight_group)  = c("Low","Mid","High")
# Change variable names
dat %>%
  rename(`Bone Metastasis` = bm,
         `Performance rating` = pf,
         `History of cardiovascular events` = hx,
         `2-year survival` = Survival,
         Weight = weight_group,
         Age = age_group) -> dat
## 2.a Mosaic plot with 2 variables -----------------------------------------
plot_mosaic(dat = 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, sep. = 0.034,
            font.size = c(10, 10, 10, 10, 0.7),
            title = NULL, lab.xy = NULL,
            strip = "Treatment effect size (log-hazard ratio)",
            col.line = "white", lwd. = 2,
            effect = "HR", print.ss = FALSE, palette = "hcl")

## 2.b Mosaic plot with 3 variables -----------------------------------------
plot_mosaic(dat = dat,
            covari.sel = c(15, 7, 4),
            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(10, 10, 10, 10, 0.7),
            title = NULL, lab.xy = NULL,
            strip = "Treatment effect size (log-hazard ratio)",
            effect = "HR", palette = "hcl")

SubgrPlots documentation built on Jan. 29, 2020, 5:07 p.m.