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Omit pedigree plot generations where both dam and sire are unknown #176

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Merged
labkey-jeckels merged 1 commit into from
Apr 30, 2021
Merged

Omit pedigree plot generations where both dam and sire are unknown #176

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17 changes: 10 additions & 7 deletions ehr/resources/reports/schemas/study/Pedigree/Pedigree.r
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Original file line number Diff line number Diff line change
Expand Up @@ -15,8 +15,7 @@ library(Rlabkey)

labkey.setCurlOptions(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)


if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.data$sire))) {
if ((length(labkey.data$id) == 0) | (is.na(labkey.data$dam) & is.na(labkey.data$sire))){
png(filename="${imgout:myscatterplot}", width = 650, height = 150);
plot(0, 0, type='n', xaxt='n', yaxt='n', bty='n', ann=FALSE )
title(main = "No pedigree data found for selected animal(s).", sub = NULL, xlab = NULL, ylab = NULL,
Expand Down Expand Up @@ -185,6 +184,8 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
return (substr(lineNL, 1, nchar(lineNL) - 1));
};

unknownIdIndex = 1

#[Quoc: remove ]
#The pedigree program expects all individuals to have either 2 parents or 1.
#Sometimes the father is not known. For missing parents we give them a unique id and
Expand All @@ -200,17 +201,19 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
if (length(damIndex) == 0) damIndex <- which(allPed$Id == ped$Dam[i]);
if (length(sireIndex) == 0) sireIndex <- which(allPed$Id == ped$Sire[i]);

if(is.na(ped$Sire[i])){
xt <- sample (1:99,1)
if((is.na(ped$Sire[i]))& (!is.na(ped$Dam[i]))){
xt <- unknownIdIndex
unknownIdIndex <- unknownIdIndex + 1
#typeof(ped$Sire);
#typeof(xt);
ped$Sire[i] <- paste('xxs',xt)
ped$Sire[i] <- paste (ped$Sire[i], "Unknown Sire", sep="\n")
#print(ped$Dam[i])
#print(ped$Sire[i])
}
if(is.na(ped$Dam[i])){
xt <- sample (1:99,1)
if((is.na(ped$Dam[i]))& (!is.na(ped$Sire[i]))){
xt <- unknownIdIndex
unknownIdIndex <- unknownIdIndex + 1
#typeof(ped$Sire);
#typeof(xt);
ped$Dam[i] <- paste ('xxd',xt);
Expand Down Expand Up @@ -302,4 +305,4 @@ if ((length(labkey.data$id) == 0) || all(is.na(labkey.data$dam) & is.na(labkey.d
legend(x = "bottomright", legend=leg.txt, pch=c(0, 1, 47), col=c('blue', 'red', 'black'), inset = 0.1, cex=1, pt.cex = 1.8)
#dev.off();
}
};
};