R/ForestBasic.r
In arnhew99/Jasper: Jasper makes plots
Defines functions
ForestBasic
Documented in
ForestBasic
ForestBasic <- function(rawdata,
LogScale=TRUE,
ExponentiateDataOnPlot=FALSE,
blanks=NULL,
Hets=NULL,
Trends=NULL,
xNoEffect=NULL,
NoEffect.lty="solid",
xaxmin,
xaxmax,
xaxis=TRUE,
ymin = 0,
ymax = par("usr")[4],
boxparmx=NULL,
boxparmy=NULL,
boxparm.stderr = NULL,
Range=NULL,
xlim=NULL,
xticks=NULL,
ticklabs=NULL,
xticks.ticklength=0.25,
mainfont=1,
xlab="",
xlab.adjust=0,
ValueLabels=TRUE,
ValueLabelsHeader="Hazard ratio",
ValueLabelsEffectSE=FALSE,
ValueDigits=NULL,
ValueDigitsSE=NULL,
separator=NULL,
NLabel=FALSE,
NLabelHeader="N",
boxsizeoverride=FALSE,
roundedSquares=FALSE,
spacing=0,
verbose=TRUE,
drawPoints=TRUE,
AdAM.mode=FALSE,
pointGroups=NULL,
pointGroupsFactor=0.9,
lwd=1,
CISecond=NULL)
{
# rawdata data.frame with columns SUBGROUP, EVENTS, HR, LCI, UCI, stderr, IsDiamond, Fill, Show, Labels, Colours
# LogScale is the x-axis on the log scale?
# blanks data.frame needing column "after"
# Hets Heterogeneity tests
# Trends Trend tests
# xNoEffect where to put the line of no effect, in user coordinates
# xaxmin where to put the left of the x-axis, in the 0-100 underlying coordinate system
# xaxmax as above, but the right hand side of the x-axis
# boxparmx parameter that defines the size of the boxes (which can be determined automatically if left NULL)
# boxparmy as above, y direction
# Range "true" range of the x-axis (user coordinates)
# xticks where to add ticks on the x-axis
# ticklabs custom tick labels at the locations given by xticks
# mainfont the overall font size from which all other font sizes are determined
# xlab x-axis label
# ValueLabels Logical, whether to show the labels to the right of the forest
# ValueLabelsHeader Title to put above the labels
# separator What separator to use between the LCI and UCI in the label
# NLabel Logical, whether to show the labels to the left of the forest
# NLabelHeader Title to put above the left labels
# boxsizeoverride Use boxparmx for every box (i.e. no adjustment in box size for stderr)
# roundedSquares Logical, use squares with rounded corners (MA thinks this looks good, you may disagree. One reason is that R draws lines with rounded ends, which is unpleasant, so we may as well be consistent)
# spacing Gap between the forest and the right hand labels (in 0-100 coordinates)
# MA: do some checks about what rawdata contains, if it has missing (but necessary) columns, then add the defaults here
# check to see if rawdata is actually a list (and if it is, reassign its contents)
if (all(is.list(rawdata), !is.data.frame(rawdata))) {
force(rawdata.orig <- rawdata)
force(rawdata <- rawdata.orig$forest)
if (!is.null(rawdata.orig$blanks)) blanks <- rawdata.orig$blanks
if (!is.null(rawdata.orig$Hets)) Hets <- rawdata.orig$Hets
if (!is.null(rawdata.orig$Trends)) Trends <- rawdata.orig$Trends
} else {
force(rawdata.orig <- rawdata)
}
if (all(is.null(Range), !is.null(xlim))) Range <- xlim
npoints <- dim(rawdata)[1]
# for reasons, we may want to be given $RR, $Estimate or $LogRR instead of HR
# so I'll just relabel them internally
if (all(is.null(rawdata$HR), !is.null(rawdata$Estimate))) {
rawdata$HR <- rawdata$Estimate
}
if (all(is.null(rawdata$HR), !is.null(rawdata$LogRR))) {
rawdata$HR <- rawdata$LogRR
}
if (all(is.null(rawdata$HR), !is.null(rawdata$RR))) {
rawdata$HR <- rawdata$RR
}
# We compute LCI and UCI from the stderr if only that has been provided, but it's not that ideal,
# because there might be some weird reason for wanting something else
if (is.null(rawdata$SUBGROUP)) {
rawdata$SUBGROUP <- rep("",npoints)
if (verbose) cat("$SUBGROUPs not specified (defaulting to 1 SUBGROUP).\n")
}
if (is.null(rawdata$LCI)) {
rawdata$LCI <- rawdata$HR - 2*rawdata$stderr
if (verbose) cat("$LCI not specified (computing from provided $stderr, care needed).\n")
}
if (is.null(rawdata$UCI)) {
rawdata$UCI <- rawdata$HR + 2*rawdata$stderr
if (verbose) cat("$UCI not specified (computing from provided $stderr, care needed).\n")
}
if (is.null(rawdata$boxsize)) {
rawdata$boxsize <- rep(1, npoints)
if (verbose) cat("$boxsize not specified, setting to 1.\n")
}
if (is.null(rawdata$EVENTS)) {
rawdata$EVENTS <- rep(100,npoints)
if (verbose) cat("$EVENTS not specified (defaulting to N=100).\n")
}
if (is.null(rawdata$IsDiamond)) {
rawdata$IsDiamond <- rep(FALSE, npoints)
if (verbose) cat("$IsDiamond not specified (defaulting to no diamonds).\n")
}
if (is.null(rawdata$DiamondGuidelines)) {
rawdata$DiamondGuidelines <- rawdata$IsDiamond
if (verbose) cat("$DiamondGuidelines not specified (any diamonds get a guideline).\n")
}
if (is.null(rawdata$Show)) {
rawdata$Show <- rep(TRUE, npoints)
if (verbose) cat("$Show not specified (defaulting to showing all).\n")
}
if (is.null(rawdata$ShowCI)) {
rawdata$ShowCI <- rep(TRUE, npoints)
if (verbose) cat("$ShowCI not specified (defaulting to showing all).\n")
}
if (is.null(rawdata$FillColour)) {
rawdata$FillColour <- rep(1, npoints)
if (verbose) cat("$FillColour not specified (defaulting to black).\n")
}
# if (is.null(rawdata$Colours)) {
# rawdata$Colours <- rep(1, npoints)
# if (verbose) cat("$Colours not specified (defaulting to black).\n")
# }
if (!("Fill" %in% names(rawdata))) {
rawdata$Fill <- rep(TRUE,npoints)
if (verbose) cat("$Fill not specified (defaulting to solid colour).\n")
}
if (is.null(Range)) {
if (LogScale) Range <- c(exp(min(rawdata$LCI)), exp(max(rawdata$UCI))) else Range <- c(min(rawdata$LCI), max(rawdata$UCI))
if (verbose) {
cat("Range not specified (making a guess).\n")
print(Range)
}
}
if (is.null(xticks)) {
xticks <- pretty(Range, n=5)
# use .Machine$double.eps here because the logic here behaves weirdly if max(Range) == max(xticks)
if (length(which(xticks - .Machine$double.eps > max(Range))) != 0) xticks <- xticks[-which(xticks > max(Range))]
if (length(which(xticks + .Machine$double.eps < min(Range))) != 0) xticks <- xticks[-which(xticks < min(Range))]
if (verbose) {
cat("xticks not specified (making a guess).\n")
print(xticks)
}
}
if (is.null(ticklabs)) {
ticklabs <- Tick_Pretty(xticks)
if (verbose) cat("ticklabs not specified (setting to xticks)\n")
}
if (is.null(separator)) {
separator <- ", "
if (verbose) cat("CI separator not specified (defaulting to ,).\n")
}
if (all(is.null(pointGroups), !is.null(rawdata.orig$pointGroups))) {
pointGroups <- rawdata.orig$pointGroups
}
# evaluate the yspacings
if (!is.null(blanks)) blanksafter = blanks$after else blanksafter = NULL
if (!is.null(Hets)) hetsafter = Hets$after else hetsafter=NULL
if (!is.null(Trends)) trendsafter = Trends$after else trendsafter = NULL
yspacing <- ONYXForestYSpacing(npoints=npoints, nhets=ifelse(is.null(Hets),0,dim(Hets)[1]), ntrends=ifelse(is.null(Trends),0,dim(Trends)[1]), nblanks=ifelse(is.null(blanks),0,dim(blanks)[1]), Ymax=ymax, Ymin=ymin, IsDiamond=rawdata$IsDiamond, StrayTextAfter=blanksafter, HetAfter=hetsafter, TrendAfter=trendsafter, AdAM.mode=AdAM.mode, pointGroups=pointGroups, pointGroupsFactor=pointGroupsFactor)
# draw the X axis
if (xaxis) ONYXForestXAxis(Range=Range, LogScale=LogScale, xNoEffect=xNoEffect, blanks=blanks, yspacing=yspacing, xaxmin=xaxmin, xaxmax=xaxmax, xticks=xticks, TickLabs=ticklabs, mainfont=mainfont, xlab=xlab, xlab.adjust=xlab.adjust, XLabelFont=1, Ymin=ymin, Ymax=ymax, lwd=lwd, tcl=xticks.ticklength, NoEffect.lty=NoEffect.lty)
npoints <- dim(rawdata)[1]
# calculate a boxparm if needed
if (is.null(boxparmx)) {
if (is.null(boxparm.stderr)) {
boxparms <- ONYXForestBoxparm(boxparm=NULL, stderr=rawdata$stderr[rawdata$Show & rawdata$ShowCI], Ymax=ymax, YLast = yspacing$YLast)
boxparmx <- boxparms$boxparmx
boxparmy <- boxparms$boxparmy
}
else {
boxparms <- CalcBoxParm(boxparm.stderr, xlim=c(xaxmin, xaxmax))
boxparmx <- boxparms[1]
boxparmy <- boxparms[2]
}
}
if (is.null(CISecond)) CISecond <- TRUE
# add the points
if (drawPoints) {
XLocs <- ONYXForestDrawPoints(estim=rawdata$HR,
lower=rawdata$LCI,
upper=rawdata$UCI,
stderr=rawdata$stderr,
boxsize=rawdata$boxsize,
LogScale = LogScale,
ExponentiateDataOnPlot=ExponentiateDataOnPlot,
npoints=npoints,
Range=Range,
xaxmin=xaxmin,
xaxmax=xaxmax,
boxparmx=boxparmx,
boxparmy=boxparmy,
YLocs=yspacing$YLocs,
YLast=yspacing$YLast,
IsDiamond=rawdata$IsDiamond,
DiamondGuidelines=rawdata$DiamondGuidelines,
Fill=rawdata$Fill,
Show=rawdata$Show,
ShowCI=rawdata$ShowCI,
PColours=rawdata$FillColour,
boxsizeoverride=boxsizeoverride,
roundedSquares=roundedSquares,
lwd=lwd,
CISecond=CISecond)
# add guidelines and N, hazard ratio infos
ONYXForestGuidelines(npoints=npoints, IsDiamond=force(rawdata$IsDiamond & rawdata$DiamondGuidelines & rawdata$Show), atvals=XLocs, YLocs=yspacing$YLocs, YLast=yspacing$YLast, blanks=blanksafter, OvlineType="dashed")
}
if (ValueLabels) {
middlevaluelabel <- ONYXForestValues(estim=rawdata$HR, upper=rawdata$UCI, lower=rawdata$LCI, stderr=rawdata$stderr, isLogged=ExponentiateDataOnPlot, xaxmax=xaxmax, YLocs=yspacing$YLocs, Boldness=ifelse(rawdata$IsDiamond,2,1), mainfont=mainfont, separator=separator, Show=rawdata$Show, ShowCI=rawdata$ShowCI, spacing=spacing, digits=ValueDigits, digits_SE=ValueDigitsSE, ValueLabelsEffectSE=ValueLabelsEffectSE)
ONYXForestValueLabels(ThisCol=ValueLabelsHeader, MidValLab=middlevaluelabel, mainfont=mainfont, Ymax=ymax)
}
if (NLabel) {
middlenevents <- ONYXForestNEvents(xaxmin=xaxmin, YLocs=yspacing$YLocs, nevents=rawdata$EVENTS, Boldness=ifelse(rawdata$IsDiamond,2,1), mainfont=mainfont)
ONYXForestNEventsLabel(EventsTit=NLabelHeader, MidNEvents=middlenevents, mainfont=mainfont)
}
return(yspacing)
}
arnhew99/Jasper documentation built on Nov. 19, 2022, 2:46 p.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions ForestBasic
Documented in ForestBasic
ForestBasic <- function(rawdata,
LogScale=TRUE,
ExponentiateDataOnPlot=FALSE,
blanks=NULL,
Hets=NULL,
Trends=NULL,
xNoEffect=NULL,
NoEffect.lty="solid",
xaxmin,
xaxmax,
xaxis=TRUE,
ymin = 0,
ymax = par("usr")[4],
boxparmx=NULL,
boxparmy=NULL,
boxparm.stderr = NULL,
Range=NULL,
xlim=NULL,
xticks=NULL,
ticklabs=NULL,
xticks.ticklength=0.25,
mainfont=1,
xlab="",
xlab.adjust=0,
ValueLabels=TRUE,
ValueLabelsHeader="Hazard ratio",
ValueLabelsEffectSE=FALSE,
ValueDigits=NULL,
ValueDigitsSE=NULL,
separator=NULL,
NLabel=FALSE,
NLabelHeader="N",
boxsizeoverride=FALSE,
roundedSquares=FALSE,
spacing=0,
verbose=TRUE,
drawPoints=TRUE,
AdAM.mode=FALSE,
pointGroups=NULL,
pointGroupsFactor=0.9,
lwd=1,
CISecond=NULL)
{
# rawdata data.frame with columns SUBGROUP, EVENTS, HR, LCI, UCI, stderr, IsDiamond, Fill, Show, Labels, Colours
# LogScale is the x-axis on the log scale?
# blanks data.frame needing column "after"
# Hets Heterogeneity tests
# Trends Trend tests
# xNoEffect where to put the line of no effect, in user coordinates
# xaxmin where to put the left of the x-axis, in the 0-100 underlying coordinate system
# xaxmax as above, but the right hand side of the x-axis
# boxparmx parameter that defines the size of the boxes (which can be determined automatically if left NULL)
# boxparmy as above, y direction
# Range "true" range of the x-axis (user coordinates)
# xticks where to add ticks on the x-axis
# ticklabs custom tick labels at the locations given by xticks
# mainfont the overall font size from which all other font sizes are determined
# xlab x-axis label
# ValueLabels Logical, whether to show the labels to the right of the forest
# ValueLabelsHeader Title to put above the labels
# separator What separator to use between the LCI and UCI in the label
# NLabel Logical, whether to show the labels to the left of the forest
# NLabelHeader Title to put above the left labels
# boxsizeoverride Use boxparmx for every box (i.e. no adjustment in box size for stderr)
# roundedSquares Logical, use squares with rounded corners (MA thinks this looks good, you may disagree. One reason is that R draws lines with rounded ends, which is unpleasant, so we may as well be consistent)
# spacing Gap between the forest and the right hand labels (in 0-100 coordinates)
# MA: do some checks about what rawdata contains, if it has missing (but necessary) columns, then add the defaults here
# check to see if rawdata is actually a list (and if it is, reassign its contents)
if (all(is.list(rawdata), !is.data.frame(rawdata))) {
force(rawdata.orig <- rawdata)
force(rawdata <- rawdata.orig$forest)
if (!is.null(rawdata.orig$blanks)) blanks <- rawdata.orig$blanks
if (!is.null(rawdata.orig$Hets)) Hets <- rawdata.orig$Hets
if (!is.null(rawdata.orig$Trends)) Trends <- rawdata.orig$Trends
} else {
force(rawdata.orig <- rawdata)
}
if (all(is.null(Range), !is.null(xlim))) Range <- xlim
npoints <- dim(rawdata)[1]
# for reasons, we may want to be given $RR, $Estimate or $LogRR instead of HR
# so I'll just relabel them internally
if (all(is.null(rawdata$HR), !is.null(rawdata$Estimate))) {
rawdata$HR <- rawdata$Estimate
}
if (all(is.null(rawdata$HR), !is.null(rawdata$LogRR))) {
rawdata$HR <- rawdata$LogRR
}
if (all(is.null(rawdata$HR), !is.null(rawdata$RR))) {
rawdata$HR <- rawdata$RR
}
# We compute LCI and UCI from the stderr if only that has been provided, but it's not that ideal,
# because there might be some weird reason for wanting something else
if (is.null(rawdata$SUBGROUP)) {
rawdata$SUBGROUP <- rep("",npoints)
if (verbose) cat("$SUBGROUPs not specified (defaulting to 1 SUBGROUP).\n")
}
if (is.null(rawdata$LCI)) {
rawdata$LCI <- rawdata$HR - 2*rawdata$stderr
if (verbose) cat("$LCI not specified (computing from provided $stderr, care needed).\n")
}
if (is.null(rawdata$UCI)) {
rawdata$UCI <- rawdata$HR + 2*rawdata$stderr
if (verbose) cat("$UCI not specified (computing from provided $stderr, care needed).\n")
}
if (is.null(rawdata$boxsize)) {
rawdata$boxsize <- rep(1, npoints)
if (verbose) cat("$boxsize not specified, setting to 1.\n")
}
if (is.null(rawdata$EVENTS)) {
rawdata$EVENTS <- rep(100,npoints)
if (verbose) cat("$EVENTS not specified (defaulting to N=100).\n")
}
if (is.null(rawdata$IsDiamond)) {
rawdata$IsDiamond <- rep(FALSE, npoints)
if (verbose) cat("$IsDiamond not specified (defaulting to no diamonds).\n")
}
if (is.null(rawdata$DiamondGuidelines)) {
rawdata$DiamondGuidelines <- rawdata$IsDiamond
if (verbose) cat("$DiamondGuidelines not specified (any diamonds get a guideline).\n")
}
if (is.null(rawdata$Show)) {
rawdata$Show <- rep(TRUE, npoints)
if (verbose) cat("$Show not specified (defaulting to showing all).\n")
}
if (is.null(rawdata$ShowCI)) {
rawdata$ShowCI <- rep(TRUE, npoints)
if (verbose) cat("$ShowCI not specified (defaulting to showing all).\n")
}
if (is.null(rawdata$FillColour)) {
rawdata$FillColour <- rep(1, npoints)
if (verbose) cat("$FillColour not specified (defaulting to black).\n")
}
# if (is.null(rawdata$Colours)) {
# rawdata$Colours <- rep(1, npoints)
# if (verbose) cat("$Colours not specified (defaulting to black).\n")
# }
if (!("Fill" %in% names(rawdata))) {
rawdata$Fill <- rep(TRUE,npoints)
if (verbose) cat("$Fill not specified (defaulting to solid colour).\n")
}
if (is.null(Range)) {
if (LogScale) Range <- c(exp(min(rawdata$LCI)), exp(max(rawdata$UCI))) else Range <- c(min(rawdata$LCI), max(rawdata$UCI))
if (verbose) {
cat("Range not specified (making a guess).\n")
print(Range)
}
}
if (is.null(xticks)) {
xticks <- pretty(Range, n=5)
# use .Machine$double.eps here because the logic here behaves weirdly if max(Range) == max(xticks)
if (length(which(xticks - .Machine$double.eps > max(Range))) != 0) xticks <- xticks[-which(xticks > max(Range))]
if (length(which(xticks + .Machine$double.eps < min(Range))) != 0) xticks <- xticks[-which(xticks < min(Range))]
if (verbose) {
cat("xticks not specified (making a guess).\n")
print(xticks)
}
}
if (is.null(ticklabs)) {
ticklabs <- Tick_Pretty(xticks)
if (verbose) cat("ticklabs not specified (setting to xticks)\n")
}
if (is.null(separator)) {
separator <- ", "
if (verbose) cat("CI separator not specified (defaulting to ,).\n")
}
if (all(is.null(pointGroups), !is.null(rawdata.orig$pointGroups))) {
pointGroups <- rawdata.orig$pointGroups
}
# evaluate the yspacings
if (!is.null(blanks)) blanksafter = blanks$after else blanksafter = NULL
if (!is.null(Hets)) hetsafter = Hets$after else hetsafter=NULL
if (!is.null(Trends)) trendsafter = Trends$after else trendsafter = NULL
yspacing <- ONYXForestYSpacing(npoints=npoints, nhets=ifelse(is.null(Hets),0,dim(Hets)[1]), ntrends=ifelse(is.null(Trends),0,dim(Trends)[1]), nblanks=ifelse(is.null(blanks),0,dim(blanks)[1]), Ymax=ymax, Ymin=ymin, IsDiamond=rawdata$IsDiamond, StrayTextAfter=blanksafter, HetAfter=hetsafter, TrendAfter=trendsafter, AdAM.mode=AdAM.mode, pointGroups=pointGroups, pointGroupsFactor=pointGroupsFactor)
# draw the X axis
if (xaxis) ONYXForestXAxis(Range=Range, LogScale=LogScale, xNoEffect=xNoEffect, blanks=blanks, yspacing=yspacing, xaxmin=xaxmin, xaxmax=xaxmax, xticks=xticks, TickLabs=ticklabs, mainfont=mainfont, xlab=xlab, xlab.adjust=xlab.adjust, XLabelFont=1, Ymin=ymin, Ymax=ymax, lwd=lwd, tcl=xticks.ticklength, NoEffect.lty=NoEffect.lty)
npoints <- dim(rawdata)[1]
# calculate a boxparm if needed
if (is.null(boxparmx)) {
if (is.null(boxparm.stderr)) {
boxparms <- ONYXForestBoxparm(boxparm=NULL, stderr=rawdata$stderr[rawdata$Show & rawdata$ShowCI], Ymax=ymax, YLast = yspacing$YLast)
boxparmx <- boxparms$boxparmx
boxparmy <- boxparms$boxparmy
}
else {
boxparms <- CalcBoxParm(boxparm.stderr, xlim=c(xaxmin, xaxmax))
boxparmx <- boxparms[1]
boxparmy <- boxparms[2]
}
}
if (is.null(CISecond)) CISecond <- TRUE
# add the points
if (drawPoints) {
XLocs <- ONYXForestDrawPoints(estim=rawdata$HR,
lower=rawdata$LCI,
upper=rawdata$UCI,
stderr=rawdata$stderr,
boxsize=rawdata$boxsize,
LogScale = LogScale,
ExponentiateDataOnPlot=ExponentiateDataOnPlot,
npoints=npoints,
Range=Range,
xaxmin=xaxmin,
xaxmax=xaxmax,
boxparmx=boxparmx,
boxparmy=boxparmy,
YLocs=yspacing$YLocs,
YLast=yspacing$YLast,
IsDiamond=rawdata$IsDiamond,
DiamondGuidelines=rawdata$DiamondGuidelines,
Fill=rawdata$Fill,
Show=rawdata$Show,
ShowCI=rawdata$ShowCI,
PColours=rawdata$FillColour,
boxsizeoverride=boxsizeoverride,
roundedSquares=roundedSquares,
lwd=lwd,
CISecond=CISecond)
# add guidelines and N, hazard ratio infos
ONYXForestGuidelines(npoints=npoints, IsDiamond=force(rawdata$IsDiamond & rawdata$DiamondGuidelines & rawdata$Show), atvals=XLocs, YLocs=yspacing$YLocs, YLast=yspacing$YLast, blanks=blanksafter, OvlineType="dashed")
}
if (ValueLabels) {
middlevaluelabel <- ONYXForestValues(estim=rawdata$HR, upper=rawdata$UCI, lower=rawdata$LCI, stderr=rawdata$stderr, isLogged=ExponentiateDataOnPlot, xaxmax=xaxmax, YLocs=yspacing$YLocs, Boldness=ifelse(rawdata$IsDiamond,2,1), mainfont=mainfont, separator=separator, Show=rawdata$Show, ShowCI=rawdata$ShowCI, spacing=spacing, digits=ValueDigits, digits_SE=ValueDigitsSE, ValueLabelsEffectSE=ValueLabelsEffectSE)
ONYXForestValueLabels(ThisCol=ValueLabelsHeader, MidValLab=middlevaluelabel, mainfont=mainfont, Ymax=ymax)
}
if (NLabel) {
middlenevents <- ONYXForestNEvents(xaxmin=xaxmin, YLocs=yspacing$YLocs, nevents=rawdata$EVENTS, Boldness=ifelse(rawdata$IsDiamond,2,1), mainfont=mainfont)
ONYXForestNEventsLabel(EventsTit=NLabelHeader, MidNEvents=middlenevents, mainfont=mainfont)
}
return(yspacing)
}
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