git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@84769 bc3139a8-67e5-0310-9ffc-ced21a209358
khansen authored on 17/12/2013 19:25:23
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@@ -1,5 +1,5 @@ |
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Package: bsseq |
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-Version: 0.11.1 |
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+Version: 0.11.2 |
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Title: Analyze, manage and store bisulfite sequencing data |
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Description: Tools for analyzing and visualizing bisulfite sequencing data |
| 5 | 5 |
Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
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@@ -82,24 +82,36 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg |
| 82 | 82 |
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| 83 | 83 |
.bsGetCol <- function(object, col, lty, lwd) {
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| 84 | 84 |
## Assumes that object has pData and sampleNames methods |
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- if(is.null(col) && "col" %in% names(pData(object))) |
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- col <- pData(object)[["col"]] |
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- else |
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- col <- rep("black", nrow(pData(object)))
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+ if(is.null(col)) {
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+ if("col" %in% names(pData(object)))
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+ col <- pData(object)[["col"]] |
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+ else |
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+ col <- rep("black", nrow(pData(object)))
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+ } |
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+ if(length(col) != nrow(object)) |
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+ col <- rep(col, length.out = nrow(object)) |
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| 89 | 93 |
if(is.null(names(col))) |
| 90 | 94 |
names(col) <- sampleNames(object) |
| 91 | 95 |
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- if(is.null(lty) && "lty" %in% names(pData(object))) |
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- lty <- pData(object)[["lty"]] |
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- else |
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- lty <- rep(1, nrow(pData(object))) |
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+ if(is.null(lty)) {
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+ if("lty" %in% names(pData(object)))
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+ lty <- pData(object)[["lty"]] |
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+ else |
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+ lty <- rep(1, nrow(pData(object))) |
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+ } |
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+ if(length(lty) != nrow(object)) |
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+ lty <- rep(lty, length.out = nrow(object)) |
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| 96 | 104 |
if(is.null(names(lty))) |
| 97 | 105 |
names(lty) <- sampleNames(object) |
| 98 | 106 |
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- if(is.null(lwd) && "lwd" %in% names(pData(object))) |
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- lwd <- pData(object)[["lwd"]] |
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- else |
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- lwd <- rep(1, nrow(pData(object))) |
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+ if(is.null(lwd)) {
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+ if("lwd" %in% names(pData(object)))
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+ lwd <- pData(object)[["lwd"]] |
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+ else |
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+ lwd <- rep(1, nrow(pData(object))) |
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+ } |
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+ if(length(lty) != nrow(object)) |
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+ lty <- rep(lty, length.out = nrow(object)) |
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| 103 | 115 |
if(is.null(names(lwd))) |
| 104 | 116 |
names(lwd) <- sampleNames(object) |
| 105 | 117 |
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| ... | ... |
@@ -5,6 +5,9 @@ |
| 5 | 5 |
\section{Version 0.11.x}{
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\itemize{
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\item Converted to using Authors@R in the DESCRIPTIOn file. |
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+ \item plotRegion did not respect the col/lty/lwd argument if given |
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+ explicitely as opposed to through pData(). Reported by Karen |
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+ Conneely <kconnee@emory.edu>. |
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| 8 | 11 |
} |
| 9 | 12 |
} |
| 10 | 13 |
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