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getSortedMinMaxStratRanges <- function(timeTree,rangesFourDate ){
#rangesFourDate <- timeTree$tipTaxonFourDateRanges
#print(rangesFourDate)
#########################
# get the ranges
rangesMinMax <- rangesFourDate[
,c("firstapp_max_ma","lastapp_min_ma")
]
rangesMinMax <- as.matrix(rangesMinMax)
rownames(rangesMinMax) <- rownames(rangesFourDate)
# transform rangesMinMax for
# same backwards timescale as tree
#rangesMinMax <- timeTree$root.time - rangesMinMax
rangesMinMaxSorted <- matrix(,Ntip(timeTree),2)
for(i in 1:Ntip(timeTree)){
whichRanges <- rownames(rangesMinMax) == (timeTree$tip.label[i])
#print(rangesMinMaxSorted);print(rangesMinMax[whichRanges,])
rangesMinMaxSorted[i,] <- rangesMinMax[whichRanges,]
}
colnames(rangesMinMaxSorted) <- c("firstMax","lastMin")
rownames(rangesMinMaxSorted) <- timeTree$tip.label
return(rangesMinMaxSorted)
}
plotTaxonStratDurations <- function(
rangesMinMax,
orientation,
XX, YY,
boxWidth = 0.7,
boxCol
){
########################
#
boxCol[is.na(boxCol)] <- "#000000FF"
#
if(orientation == "rightwards"){
for(i in 1:nrow(rangesMinMax)){
yCent <- YY[i]
ageMax <- rangesMinMax[i,"firstMax"]
ageMin <- rangesMinMax[i,"lastMin"]
#print(c(ageMax,ageMin,yCent))
#points(ageMax,yCent,cex=2)
#
graphics::rect(
xleft = ageMax,
xright = ageMin,
ytop = yCent + (boxWidth/2),
ybottom = yCent - (boxWidth/2),
col = boxCol[i],
border = boxCol[i]
)
# get new xx and yy for end of ranges
XX[i] <- ageMin
YY[i] <- yCent
}
}
if(orientation == "upwards"){
for(i in 1:nrow(rangesMinMax)){
xCent <- XX[i]
ageMax <- rangesMinMax[i,"firstMax"]
ageMin <- rangesMinMax[i,"lastMin"]
graphics::rect(
ytop = ageMin,
ybottom = ageMax,
xleft = xCent - (boxWidth/2),
xright = xCent + (boxWidth/2),
col = boxCol[i],
border = boxCol[i]
)
# get new xx and yy for end of ranges
XX[i] <- xCent
YY[i] <- ageMin
}
}
# return newXX,YY
newXY <- list(XX = XX, YY = YY)
return(newXY)
}
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