ggplot_sieve: Plotting Univariate Mark-Specific Proportional Hazards Model...
In sievePH: Sieve Analysis Methods for Proportional Hazards Models

View source: R/ggplot_sieve.R

ggplot_sieve

R Documentation

Plotting Univariate Mark-Specific Proportional Hazards Model Fits Using `ggplot`

Description

ggplot-style plotting for univariate marks. Point and interval estimates of the mark-specific treatment effect parameter specified by component contrast in summary.sievePH are plotted, together with scatter and box plots of the observed mark values by treatment.

Usage

ggplot_sieve(
  x,
  mark = NULL,
  tx = NULL,
  xlim = NULL,
  ylim = NULL,
  xtickAt = NULL,
  xtickLab = NULL,
  ytickAt = NULL,
  ytickLab = NULL,
  tickLabSize = 14,
  xlab = NULL,
  ylab = NULL,
  axisLabSize = 15,
  title = NULL,
  titleSize = 16,
  subtitle = NULL,
  subtitleSize = 10,
  txLab = c("Placebo", "Treatment"),
  txLabSize = 5,
  legendLabSize = 12,
  legendPosition = c(0.96, 1.08),
  legendJustification = c(1, 1),
  estLineSize = 1.6,
  ciLineSize = 1.2,
  boxplotWidth = 0.8,
  jitterFactor = 0.1,
  jitterSeed = 0,
  pointColor = c("blue", "red3"),
  pointSize = 1.7,
  bottomPlotMargin = c(-0.5, 0.3, 0, 0),
  topPlotMargin = c(0, 0.3, -0.12, 1.83),
  plotHeights = c(0.33, 0.67)
)

Arguments

`x`	an object returned by `summary.sievePH`
`mark`	a numeric vector specifying a univariate continuous mark. For subjects with a right-censored time-to-event, the value(s) in `mark` should be set to `NA`.
`tx`	a numeric vector indicating the treatment group (1 if treatment, 0 if placebo)
`xlim`	a numeric vector of length 2 specifying the x-axis range (`NULL` by default)
`ylim`	a numeric vector of length 2 specifying the y-axis range (`NULL` by default)
`xtickAt`	a numeric vector specifying the position of x-axis tickmarks (`NULL` by default)
`xtickLab`	a numeric vector specifying labels for tickmarks listed in `xtickAt`. If `NULL` (default), the labels are determined by `xtickAt`.
`ytickAt`	a numeric vector specifying the position of y-axis tickmarks (`NULL` by default)
`ytickLab`	a numeric vector specifying labels for tickmarks listed in `ytickAt`. If `NULL` (default), the labels are determined by `ytickAt`.
`tickLabSize`	a numeric value specifying the font size of tickmark labels along both axes in the bottom panel (`14` by default)
`xlab`	a character string specifying the x-axis label (`NULL` by default)
`ylab`	a character string specifying the y-axis label (`NULL` by default)
`axisLabSize`	a numeric value specifying the font size of both axis labels in the bottom panel (`15` by default)
`title`	a character string specifying the plot title (`NULL` by default)
`titleSize`	a numeric value specifying the font size of the plot title (`16` by default)
`subtitle`	a character string specifying the plot subtitle (`NULL` by default)
`subtitleSize`	a numeric value specifying the font size of the plot subtitle (`10` by default)
`txLab`	a character vector of length 2 specifying the placebo and treatment labels (in this order). The default labels are `placebo` and `treatment`.
`txLabSize`	a numeric value specifying the font size of labels `txLab` (`5` by default)
`legendLabSize`	a numeric value specifying the font size of legend labels in the bottom panel (`11` by default)
`legendPosition`	a numeric vector of length 2 specifying the position of the legend in the bottom panel (`c(0.96, 1.08)` by default), passed on to argument `legend.position` in `theme()`
`legendJustification`	a numeric vector of length 2 specifying the justification of the legend in the bottom panel (`c(1, 1)` by default), passed on to argument `legend.justification` in `theme()`
`estLineSize`	a numeric value specifying the line width for the point estimate of the mark-specific treatment effect (`1.6` by default)
`ciLineSize`	a numeric value specifying the line width for the confidence limits for the mark-specific treatment effect (`1.2` by default)
`boxplotWidth`	a numeric value specifying the width of each box in the box plot (`0.8`) by default
`jitterFactor`	a numeric value specifying the amount of vertical jitter (`0.1` by default)
`jitterSeed`	a numeric value setting the seed of R's random number generator for jitter in the scatter plot (`0` by default)
`pointColor`	a character vector of length 2 color-coding the placebo and treatment group (in this order) in the scatter plot (`c("blue", "red3")` by default)
`pointSize`	a numeric value specifying the size of data points in the scatter plot (`1.7` by default)
`bottomPlotMargin`	a numeric vector, using cm as the unit, passed on to argument `plot.margin` in `theme()` for the bottom panel (`c(-0.5, 0.3, 0, 0)` by default)
`topPlotMargin`	a numeric vector, using `"lines"` as the unit, passed on to argument `plot.margin` in `theme()` for the top panel (`c(0, 0.3, -0.12, 1.83)` by default)
`plotHeights`	a numeric vector specifying relative heights of the top and bottom panels (`c(0.33, 0.67)` by default) passed on to argument `heights` in `ggpubr::ggarrange()`

Value

A ggplot object.

Examples

n <- 500
tx <- rep(0:1, each=n/2)
tm <- c(rexp(n/2, 0.2), rexp(n/2, 0.2 * exp(-0.4)))
cens <- runif(n, 0, 15)
eventTime <- pmin(tm, cens, 3)
eventInd <- as.numeric(tm <= pmin(cens, 3))
mark <- ifelse(eventInd==1, c(rbeta(n/2, 2, 5), rbeta(n/2, 2, 2)), NA)
markRng <- range(mark, na.rm=TRUE)

# fit a model with a univariate mark
fit <- sievePH(eventTime, eventInd, mark, tx)
sfit <- summary(fit, markGrid=seq(markRng[1], markRng[2], length.out=10))
print(ggplot_sieve(sfit, mark, tx))

sievePH documentation built on Feb. 16, 2023, 9:55 p.m.