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Fall back to unaligned pedigree plot when kinship2 alignment fails #1147

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Fall back to unaligned pedigree plot when kinship2 alignment fails #1147

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14 changes: 13 additions & 1 deletion ehr/resources/reports/schemas/study/Pedigree/Pedigree.r
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Expand Up @@ -300,7 +300,19 @@ if ((nrow(labkey.data) == 0) | (all(is.na(labkey.data$dam)) & all(is.na(labkey.d
png(filename="${imgout:png_pedigree}", width = plotWidth, height=plotHeight);
par(xpd=TRUE);

plot(ptemp, align=T, width=15, symbolsize=symSize, cex=cexSize, col=fixedPed$colors, mar=c(4.1,3.5,4.1,3.8))
# kinship2's QP-based alignment (align=TRUE) can fail with "constraints are inconsistent,
# no solution!" on deep/looped pedigrees. Fall back to the unaligned layout in that case so
# the report still renders rather than aborting.
tryCatch(
plot(ptemp, align=TRUE, width=15, symbolsize=symSize, cex=cexSize, col=fixedPed$colors, mar=c(4.1,3.5,4.1,3.8)),
error = function(e) {
# Only the QP alignment failure is recoverable by dropping alignment; re-raise anything else.
if (!grepl("constraints are inconsistent", conditionMessage(e), fixed = TRUE))
stop(e)
message("Pedigree alignment failed (", conditionMessage(e), "); retrying with align=FALSE.")
plot(ptemp, align=FALSE, width=15, symbolsize=symSize, cex=cexSize, col=fixedPed$colors, mar=c(4.1,3.5,4.1,3.8))
}
)
mtext("Unknown animals are marked with xxs ## or xxd ## where ## is a randomly generated unique number. This identifier is used only in this plot and is re-generated each time the plot is rendered.",
side = 1, font = 3, cex = 0.95)
leg.txt <- c("Male", "Female", "Deceased")
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