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Update RCircosGenomicData.R #1

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76 changes: 41 additions & 35 deletions R/RCircosGenomicData.R
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Original file line number Diff line number Diff line change
Expand Up @@ -549,44 +549,50 @@ RCircos.Get.Data.Point.Height <- function(plot.values=NULL, min.value=NULL,

RCircos.Get.Plot.Layers <- function(genomic.data=NULL, genomic.columns=NULL)
{
if(is.null(genomic.data))
stop("Missing argument in RCircos.Check.Position.Overlaps().\n");
if(is.null(genomic.columns) || genomic.columns != 3)
stop("Start and end position are needed for layer assignment.\n");

theLayer <- 1;
theChr <- as.character(genomic.data[1, 1]);
theStart <- as.numeric(genomic.data[1, 2]);
theEnd <- as.numeric(genomic.data[1, 3]);

segLayers <- rep(1, nrow(genomic.data));
for(aRow in seq_len(nrow(genomic.data))[-1])
{
# Meet a new region without overlap with previous or
# a different chromosome, reset relevant variables
# ==================================================
#
if (genomic.data[aRow, 2] >= theEnd ) {
theLayer <- 1;
theStart <- genomic.data[aRow, 2];
theEnd <- genomic.data[aRow, 3];
} else if (genomic.data[aRow, 1] != theChr) {
theLayer <- 1;
theChr <- genomic.data[aRow, 1];
theStart <- genomic.data[aRow, 2];
theEnd <- genomic.data[aRow, 3];
} else {
theLayer <- theLayer + 1;
if(genomic.data[aRow, 3] > theEnd)
{ theEnd <- genomic.data[aRow, 3]; }
}
segLayers[aRow] <- theLayer;
if(is.null(genomic.data))
stop("Missing argument in RCircos.Check.Position.Overlaps().\n");
if(is.null(genomic.columns) || genomic.columns != 3)
stop("Start and end position are needed for layer assignment.\n");
genomic.data <- genomic.data[order(genomic.data[,2]),]; # order by start position
theLayer <- 1;
theChr <- as.character(genomic.data[1, 1]);
theStart <- as.numeric(genomic.data[1, 2]);
theEnd <- as.numeric(genomic.data[1, 3]);
nestedEnd1 <- as.numeric(genomic.data[1, 3]);
nestedEnd2 <- as.numeric(genomic.data[1, 3]);
segLayers <- rep(1, nrow(genomic.data));
for(aRow in seq_len(nrow(genomic.data))[-1]) {
# Meet a new region without overlap with previous or
# a different chromosome, reset relevant variables
# ==================================================
#
if (genomic.data[aRow, 2] >= theEnd ) { # if end of tile n-1 does not overlap tile n range. set to 1 and update new end
theLayer <- 1;
theStart <- genomic.data[aRow, 2];
theEnd <- genomic.data[aRow, 3];
} else if (genomic.data[aRow, 1] != theChr) {
theLayer <- 1;
theChr <- genomic.data[aRow, 1];
theStart <- genomic.data[aRow, 2];
theEnd <- genomic.data[aRow, 3];
} else { # if end of tile n-1 does overlap tile n
if(genomic.data[aRow, 2] >= nestedEnd1){ # if we are nested once
nestedEnd1 <- genomic.data[aRow, 3]; # update end
theLayer <- 2;
} else if(genomic.data[aRow, 2] >= nestedEnd2){ # if we are nested twice
nestedEnd2 <- genomic.data[aRow, 3]; # update end
theLayer <- 3;
}
if(genomic.data[aRow, 3] > theEnd)
{ theEnd <- genomic.data[aRow, 3]; }
}

return(segLayers);
segLayers[aRow] <- theLayer;
}
return(segLayers);
}



# End of RCircosGenomicData.R
# ________________________________________________________________________
# <RCircos><RCircos><RCircos><RCircos><RCircos><RCircos><RCircos><RCircos>
# <RCircos><RCircos><RCircos><RCircos><RCircos><RCircos><RCircos><RCircos>