documentation updates

genome · Mar 21, 2016 · efd67e4 · efd67e4
1 parent d0f066b
commit efd67e4
Show file tree

Hide file tree

Showing 3 changed files with 31 additions and 9 deletions.
diff --git a/man/sc.plot1d.Rd b/man/sc.plot1d.Rd
@@ -11,7 +11,8 @@
                 positionsToHighlight=NULL, highlightsHaveNames=FALSE,
                 overlayClusters=TRUE, overlayIndividualModels=TRUE,
                 showHistogram=FALSE, showTitle=TRUE,
-                biggerText=FALSE, highlightsOnHistogram=FALSE)
+                biggerText=FALSE, highlightsOnHistogram=FALSE,
+                highlightCnPoints=FALSE)
 
 }
 \arguments{
@@ -33,6 +34,13 @@
     sex-chromosome variants using a different plotting emblem than that
     used for other data points (a triangle is currently used)
   }
+  \item{highlightCnPoints}{
+    boolean argument to decide whether or not to highlight all
+    variants with chromosome specified as "CN". This is intended to be
+    used when including pseudo-vafs from CN events detected with
+    external methods. Points are highlighted by using a square for the
+    plotting emblem.
+  }
   \item{positionsToHighlight}{
     a list of positions in 2-column format 1) chromosome 2) position.
     These points will be highlighted on the output scatterplot by using

diff --git a/man/sc.plot2d.Rd b/man/sc.plot2d.Rd
@@ -6,13 +6,15 @@
 \description{
   Creates a pdf with one plot for each pair of samples.
 }
-\usage{sc.plot2d(sco, outputFile, positionsToHighlight=NULL,
+\usage{sc.plot2d(sco, outputFile=NULL, positionsToHighlight=NULL,
                  highlightsHaveNames=FALSE, overlayClusters=TRUE,
                  overlayErrorBars=FALSE, ellipse.metadata = list(),
                  singlePage=FALSE, scale=1, xlim=100, ylim=100,
-                 plot.title="Plot Title", clusterLegend=TRUE,
-                 flipSamples=FALSE, xlab="Tumor 1 VAF",
-                 ylab="Tumor 2 VAF", colors=c("red","blue","green"))
+                 plot.title=NULL, samplesToPlot=NULL,
+                 clusterLegend=TRUE, 
+                 flipSamples=FALSE, xlab=NULL,
+                 ylab=NULL, colors=NULL,
+                 plotWidth=7.2, plotHeight=6)
 
 }
 \arguments{
@@ -23,6 +25,10 @@
     path/name of pdf file that will contain the plots. Optional, but 
     generally recommended, especially if you have more than two samples
   }
+  \item{samplesToPlot}{
+    a list of sample names that should be included in the 2d
+    plots. Default is to plot allcombinations of all samples.
+  }
   \item{overlayClusters}{
     boolean argument to decide whether to overlay cluster designations
     on the standard scatterplot output
@@ -75,15 +81,22 @@
   }
  \item{clusterLegend}{
    add a legend showing cluster numbers (TRUE/FALSE)
- } 
+ }
+ \item{plotWidth}{
+   width of the pdf (in inches) that is produced (default 7.2)
+ }
+ \item{plotHeight}{
+   height of the pdf (in inches)that is produced (default 6)
+ }
+
 }  
 \details{  
   Creates a scatter plot for each pairing of samples, with clusters
   indicated by color and shape.
 }
 
 \value{
-  does not return anything, creates pdf file
+  does not return anything, creates pdf file or output plot
 }
 
 \examples{

diff --git a/man/sciClone.Rd b/man/sciClone.Rd
@@ -12,8 +12,9 @@
 \usage{
     sciClone(vafs, copyNumberCalls=NULL, regionsToExclude=NULL,
              sampleNames, minimumDepth=100, clusterMethod="bmm",
-             clusterParams=NULL, cnCallsAreLog2=FALSE,
-             useSexChrs=TRUE, doClustering=TRUE, verbose=TRUE,
+             clusterParams="no.apply.overlapping.std.dev.condition",
+             cnCallsAreLog2=FALSE, useSexChrs=TRUE, doClustering=TRUE,
+             verbose=TRUE, 
              copyNumberMargins=0.25, maximumClusters=10,
              annotation=NULL, doClusteringAlongMargins=TRUE,
              plotIntermediateResults=0)