plotConfidence: Plot confidence intervals

In Publish: Format Output of Various Routines in a Suitable Way for Reports and Publication

Plot confidence intervals

Description

Function to plot confidence intervals with their values and additional labels. One anticipated use of this function involves first the generation of a regression object, then arrangement of a result table with "regressionTable", further arrangment of table with with e.g. "fixRegressionTable" and various user defined changes - and then finally table along with forest plot using the current function.

Usage

plotConfidence(
  x,
  y.at,
  lower,
  upper,
  pch = 16,
  cex = 1,
  lwd = 1,
  col = 4,
  xlim,
  xlab,
  labels,
  title.labels,
  values,
  title.values,
  section.pos,
  section.sep,
  section.title = NULL,
  section.title.x,
  section.title.offset,
  order,
  leftmargin = 0.025,
  rightmargin = 0.025,
  stripes,
  factor.reference.pos,
  factor.reference.label = "Reference",
  factor.reference.pch = 16,
  refline = 1,
  title.line = TRUE,
  xratio,
  y.offset = 0,
  y.title.offset,
  digits = 2,
  format,
  extremearrows.length = 0.05,
  extremearrows.angle = 30,
  add = FALSE,
  layout = TRUE,
  xaxis = TRUE,
  ...
)

Arguments

x	Either a vector containing the point estimates or a list whose first element contains the point estimates. Further list elements can contain the confidence intervals and labels. In this case the list needs to have names 'lower' and 'upper' to indicate the values of the lower and the upper limits of the confidence intervals, respectively, and may have an element 'labels' which is a vector or matrix or list with labels.
y.at	Optional vector of y-position for the confidence intervals and corresponding values and labels.
lower	Lower confidence limits. Used if object x is a vector and if x is a list lower overwrites element x$lower.
upper	Upper confidence limits. Used if object x is a vector and if x is a list upper overwrites element x$upper.
pch	Symbol for points.
cex	Defaults size of all figures and plotting symbol. Single elements are controlled separately. See ....
lwd	Default width of all lines Single elements are controlled separately. See ....
col	Default colour of confidence intervals.
xlim	Plotting limits for the confidence intervals. See also xratio on how to control the layout.
xlab	Label for the x-axis.
labels	Vector or matrix or list with labels. Used if object x is a vector and if x is a list it overwrites element x$labels. To avoid drawing of labels, set labels=FALSE.
title.labels	Main title for the column which shows the labels. If labels is a matrix or list title.labels should be a vector with as many elements as labels has columns or elements.
values	Either logical or vector, matrix or list with values. If values=TRUE values are constructed according to format from lower and upper overwrites constructed values. If values=FALSE do not draw values.
title.values	Main title for the column values. If values is a matrix or list title.labels should be a vector with as many elements as values has columns or elements.
section.pos	Vector with y-axis posititions for section.titles.
section.sep	Amount of space between paragraphs (applies only if labels is a named list)
section.title	Intermediate section headings.
section.title.x	x-position for section.titles
section.title.offset	Y-offset for section.titles
order	Order of the three columns: labels, confidence limits, values. See examples.
leftmargin	Percentage of plotting region used for leftmargin. Default is 0.025. See also Details.
rightmargin	Percentage of plotting region used for rightmargin. Default is 0.025. See also Details.
stripes	Vector of up to three Logicals. If TRUE draw stripes into the background. The first applies to the labels, the second to the graphical presentation of the confidence intervals and the third to the values. Thus, stripes
factor.reference.pos	Position at which factors attain reference values.
factor.reference.label	Label to use at factor.reference.pos instead of values.
factor.reference.pch	Plotting symbol to use at factor.reference.pos
refline	Position of a vertical line to indicate the null hypothesis. Default is 1 which would work for odds ratios and hazard ratios.
title.line	Position of a horizontal line to separate the title line from the plot
xratio	One or two values between 0 and 1 which determine how to split the plot window in horizontal x-direction. If there are two columns (labels, CI) or (CI, values) only one value is used and the default is 0.618 (goldener schnitt) which gives the graphical presentation of the confidence intervals 38.2 graph. The remaining 61.8 If there are three columns (labels, CI, values), xratio has two values which default to fractions of 0.7 according to the relative widths of labels and values, thus by default only 0.3 are used for the graphical presentation of the confidence intervals. The remaining 30 confidence intervals. See examles.
y.offset	Either a single value or a vector determining the vertical offset of all rows. If it is a single value all rows are shifted up (or down if negative) by this value. This can be used to add a second set of confidence intervals to an existing graph or to achieve a visual grouping of rows that belong together. See examples.
y.title.offset	Numeric value by which to vertically shift the titles of the labels and values.
digits	Number of digits, passed to pubformat and formatCI.
format	Format for constructing values of confidence intervals. Defaults to '(u;l)' if there are negative lower or upper values and to '(u-l)' otherwise.
extremearrows.length	Length of the arrows in case of confidence intervals that stretch beyond xlim.
extremearrows.angle	Angle of the arrows in case of confidence intervals that stretch beyond xlim.
add	Logical. If TRUE do not draw labels or values and add confidence intervals to existing plot.
layout	Logical. If FALSE do not call layout. This is useful when several plotConfidence results should be combined in one graph and hence layout is called externally.
xaxis	Logical. If FALSE do not draw x-axis.
...	Used to control arguments of the following subroutines: plot: Applies to plotting frame of the graphical presentation of confidence intervals. Use arguments of plot, e.g., plot.main="Odds ratio". points, arrows: Use arguments of points and arrows, respectively. E.g., points.pch=8 and arrows.lwd=2. refline: Use arguments of segments, e.g., refline.lwd=2. See segments. labels, values, title.labels, title.values: Use arguments of text, e.g., labels.col="red" or title.values.cex=1.8. xaxis: Use arguments of axis, e.g., xaxis.at=c(-0.3,0,0.3) xlab: Use arguments of mtext, e.g., xlab.line=2. stripes: Use arguments of stripes. See examples. See examples for usage.

Details

Function to plot means and other point estimates with confidence intervals, their values and additional labels . Horizonal margins as determined by par()$mar are ignored. Instead layout is used to divide the plotting region horizontally into two or three parts plus leftmargin and rightmargin.

When values is FALSE there are only two parts. The default order is labels on the left confidence intervals on the right. When no labels are given or labels is FALSE there are only two parts. The default order is confidence intervals on the left values on the right.

The default order of three parts from left to right is labels, confidence intervals, values. The order can be changed as shown by the examples below. The relative widths of the two or three parts need to be adapted to the actual size of the text of the labels. This depends on the plotting device and the size of the font and figures and thus has to be adjusted manually.

Oma can be used to further control horizontal margins, e.g., par(oma=c(0,4,0,4)).

If confidence limits extend beyond the range determined by xlim, then arrows are drawn at the x-lim borders to indicate that the confidence limits continue.

Value

List of dimensions and coordinates

Author(s)

Thomas A. Gerds <[e-mail]>

Examples

library(Publish)
data(CiTable) 

## A first draft version of the plot is obtained as follows
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper","p")],
          labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")])

## if argument labels is a named list the table is subdivided:
labellist <- split(CiTable[,c("Dose","Time","Mean","SD","n")],CiTable[,"Drug"])
labellist
## the data need to be ordered accordingly
CC= data.table::rbindlist(split(CiTable[,c("HazardRatio","lower","upper")],CiTable[,"Drug"]))
plotConfidence(x=CC, labels=labellist)


## The graph consist of at most three columns:
##
## column 1: labels
## column 2: printed values of the confidence intervals
## column 3: graphical presentation of the confidence intervals
##
## NOTE: column 3 appears always, the user decides if also
##       column 1, 2 should appear
##
## The columns are arranged with the function layout
## and the default order is 1,3,2 such that the graphical
## display of the confidence intervals appears in the middle
##
## the order of appearance of the three columns can be changed as follows
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               order=c(1,3,2))
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               order=c(2,3,1))
## if there are only two columns the order is 1, 2
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               values=FALSE,
               order=c(2,1))
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               values=FALSE,
               order=c(1,2))



## The relative size of the columns needs to be controlled manually
## by using the argument xratio. If there are only two columns
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xratio=c(0.4,0.15))

## The amount of space on the left and right margin can be controlled
## as follows:
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xratio=c(0.4,0.15),
               leftmargin=0.1,rightmargin=0.00)

## The actual size of the current graphics device determines
## the size of the figures and the space between them.
## The sizes and line widths are increased as follows:
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               xlab="Hazard ratio",
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               points.cex=3,
               cex=2,
               lwd=3,
               xaxis.lwd=1.3,
               xaxis.cex=1.3)
## Note that 'cex' of axis ticks is controlled via 'par' but
## cex of the label via argument 'cex' of 'mtext'.
## The sizes and line widths are decreased as follows:
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               cex=0.8,
               lwd=0.8,
               xaxis.lwd=0.8,
               xaxis.cex=0.8)

## Another good news is that all figures can be controlled separately

## The size of the graphic device can be controlled in the usual way, e.g.:
## Not run: 
    pdf("~/tmp/testCI.pdf",width=8,height=8)
    plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
                   labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")])
    dev.off()

## End(Not run)

## More control of the x-axis and confidence intervals that
## stretch outside the x-range end in an arrow. 
## the argument xlab.line adjusts the distance of the x-axis
## label from the graph
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               xlab="Hazard ratio",
               xlab.line=1.8,
               xaxis.at=c(0.8,1,1.3),
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xlim=c(0.8,1.3))

## log-scale
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               xlab="Hazard ratio",
               xlab.line=1.8,
               xaxis.at=c(0.8,1,1.3),
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xlim=c(0.8,1.3),plot.log="x")
## More pronounced arrows
## Coloured xlab expression
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               xlab=expression(HR[1](s)),
               xlab.line=1.8,
               xlab.col="darkred",
               extremearrows.angle=50,
               extremearrows.length=0.1,
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xlim=c(0.8,1.3))

## Controlling the labels and their titles
## and the values and their titles
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xlab="Hazard ratio",
               title.values=expression(bold(HR (CI[95]))),
               title.labels=c("Drug/Time","Dose","Mean","St.dev.","N"),
               factor.reference.pos=c(1,10,19),
               factor.reference.pch=16,
               cex=1.3,
               xaxis.at=c(0.75,1,1.25,1.5,2))

## For factor reference groups, one may want to replace the
## confidence intervals by the word Reference, as in the previous example.
## To change the word 'Reference' we use the argument factor.reference.label:
## To change the plot symbol for the reference lines factor.reference.pch
## To remove the plot symbol in the reference lines use 'NA' as follows:
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xlab="Hazard ratio",
               factor.reference.label="Ref",
               title.values=expression(bold(HR (CI[95]))),
               title.labels=c("Drug/Time","Dose","Mean","St.dev.","N"),
               factor.reference.pos=c(1,10,19),
               factor.reference.pch=NA,
               cex=1.3,
               xaxis.at=c(0.75,1,1.25,1.5,2))


## changing the style of the graphical confidence intervals
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               xlab="Hazard ratio",
               factor.reference.pos=c(1,10,19),
               points.pch=15,
               points.col=rainbow(27),
               points.cex=2,
               arrows.col="darkblue",
               cex=1.3,
               order=c(1,3,2),
               xaxis.at=c(0.75,1,1.25,1.5))

## the values column of the graph can have multiple columns as well
## to illustrate this we create the confidence intervals
## before calling the function and then cbind them
## to the pvalues
HR <- pubformat(CiTable[,6])
CI95 <- formatCI(lower=CiTable[,7],upper=CiTable[,8],format="(l-u)")
pval <- format.pval(CiTable[,9],digits=3,eps=10^{-3})
pval[pval=="NA"] <- ""
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               values=list("HR"=HR,"CI-95"=CI95,"P-value"=pval),
               cex=1.2,
               xratio=c(0.5,0.3))

## Finally, vertical columns can be delimited with background color
## NOTE: this may slow things down and potentially create
##       large figures (many bytes)
col1 <- rep(c(prodlim::dimColor("green",density=22),
              prodlim::dimColor("green")),length.out=9)
col2 <- rep(c(prodlim::dimColor("orange",density=22),
              prodlim::dimColor("orange")),length.out=9)
col3 <- rep(c(prodlim::dimColor("blue",density=22),
              prodlim::dimColor("blue")),length.out=9)
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               stripes=c(1,0,1),
               stripes.col=c(col1,col2,col3))
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               stripes=c(1,1,1),
               stripes.col=c(col1,col2,col3))

threegreens <- c(prodlim::dimColor("green",density=55),
                 prodlim::dimColor("green",density=33),
                 prodlim::dimColor("green",density=22))
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
               labels=CiTable[,c("Drug.Time","Dose","Mean","SD","n")],
               values=FALSE,
               xlim=c(0.75,1.5),
               stripes=c(1,1,1),
               xratio=c(0.5,0.15),
               stripes.horizontal=c(0,9,18,27)+0.5,
               stripes.col=threegreens)

# combining multiple plots into one
layout(t(matrix(1:5)))
plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
       labels=CiTable[,c("Mean","n")],
       layout=FALSE)
 plotConfidence(x=CiTable[,c("HazardRatio","lower","upper")],
       layout=FALSE)

Publish documentation built on Jan. 18, 2023, 1:08 a.m.