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fixed an issue introduced by previous commit, observed and fixed proposed by Tim Triche Jr.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/bsseq@86091 bc3139a8-67e5-0310-9ffc-ced21a209358

Kasper D. Hansen authored on 05/02/2014 03:40:31
Showing5 changed files

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@@ -1,5 +1,5 @@
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 Package: bsseq
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-Version: 0.11.2
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+Version: 0.11.3
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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
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 Authors@R: c(person(c("Kasper", "Daniel"), "Hansen", role = c("aut", "cre"),
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@@ -88,8 +88,8 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg
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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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+    if(length(col) != ncol(object))
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+        col <- rep(col, length.out = ncol(object))
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     if(is.null(names(col)))
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         names(col) <- sampleNames(object)
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@@ -97,10 +97,10 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg
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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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+            lty <- rep(1, ncol(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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+    if(length(lty) != ncol(object))
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+        lty <- rep(lty, length.out = ncol(object))
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     if(is.null(names(lty)))
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         names(lty) <- sampleNames(object)
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@@ -110,8 +110,8 @@ plotManyRegions <- function(BSseq, regions = NULL, extend = 0, main = "", addReg
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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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+    if(length(lty) != ncol(object))
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+        lty <- rep(lty, length.out = ncol(object))
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     if(is.null(names(lwd)))
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         names(lwd) <- sampleNames(object)
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@@ -7,7 +7,10 @@
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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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+    Conneely <kconnee@emory.edu>.
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+    \item Fixed an issue introduced by the previous change (to
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+    plotRegion).  Reported (with a fix) by Tim Triche Jr
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+    <tim.triche@gmail.com>.
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   }
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 }
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@@ -4,6 +4,7 @@
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 \alias{BSseqTstat}
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 \alias{BSseqTstat-class}
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 \alias{[,BSseqTstat-method}
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+\alias{[,BSseqTstat,ANY-method}
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 \alias{show,BSseqTstat-method}
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 \title{Class BSseqTstat}
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 \description{
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@@ -3,6 +3,7 @@
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 \docType{class}
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 \alias{hasGRanges-class}
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 \alias{[,hasGRanges-method}
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+\alias{[,hasGRanges,ANY-method}
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 \alias{end,hasGRanges-method}
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 \alias{end<-,hasGRanges-method}
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 \alias{granges,hasGRanges-method}