@@ -39,7 +39,7 @@ include the set size (set_size), combination size (comb_size), degree (deg).}

 \item{set_order}{Array specifying order of states.}

-\item{...}{Further arguments passed to \code{\link[UpSet]{UpSet}}}

+\item{...}{Further arguments passed to \code{\link[ComplexHeatmap]{UpSet}}}

 }

 \value{

 Returns a \code{ComplexHeatmap} object.

@@ -39,7 +39,7 @@ include the set size (set_size), combination size (comb_size), degree (deg).}

 \item{set_order}{Array specifying order of states.}

-\item{...}{further arguments passed to \code{\link[Rtsne]{Rtsne}}}

+\item{...}{Further arguments passed to \code{\link[UpSet]{UpSet}}}

 }

 \value{

 Returns a \code{ComplexHeatmap} object.

@@ -8,10 +8,10 @@ plotUpSet(

   object,

   assay = "significant",

   name = "colnames",

-  min_shared = 10,

-  min_degree = 2,

-  max_degree = NULL,

-  annotate_by = NULL,

+  minShared = 10,

+  minDegree = 2,

+  maxDegree = NULL,

+  annotateColsBy = NULL,

   comb_order = "comb_size",

   set_order = order(ss),

   ...

@@ -25,13 +25,13 @@ plotUpSet(

 \item{name}{character specifying the column in colData to use to label rows

 and columns. Default is colnames(qtle).}

-\item{min_shared}{minimum number of shared QTL for set to be included.}

+\item{minShared}{minimum number of shared QTL for set to be included.}

-\item{min_degree}{minimum degree of sharing for set to be included.}

+\item{minDegree}{minimum degree of sharing for set to be included.}

-\item{max_degree}{maximum degree of sharing for set to be included.}

+\item{maxDegree}{maximum degree of sharing for set to be included.}

-\item{annotate_by}{character or array of characters specifying the

+\item{annotateColsBy}{character or array of characters specifying the

 column(s) in colData to be plotted as annotations.}

 \item{comb_order}{characters specifying how sets should be ordered. Options

@@ -50,10 +50,10 @@ significant in sets of states.

 }

 \examples{

 sim <- qtleSimulate(

-    nstates=10, nfeatures=100, ntests=1000,

+    nStates=10, nFeatures=100, nTests=1000,

     global=0.2, multi=0.4, unique=0.2, k=2)

 sim <- callSignificance(sim, mode="simple", assay="lfsrs", 

-    thresh=0.0001, second.thresh=0.0002)

+    thresh=0.0001, secondThresh=0.0002)

 sim_sig <- getSignificant(sim)

 sim_top <- getTopHits(sim_sig, assay="lfsrs", mode="state")

 sim_top <- runPairwiseSharing(sim_top)

@@ -61,5 +61,5 @@ sim_top <- runPairwiseSharing(sim_top)

 plotUpSet(sim_top)

 # Upset plot with complex row annotations

-plotUpSet(sim_top, annotate_by = c("nSignificant", "multistateGroup"))

+plotUpSet(sim_top, annotateColsBy = c("nSignificant", "multistateGroup"))

 }

new file mode 100644

@@ -0,0 +1,65 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/plots.R

+\name{plotUpSet}

+\alias{plotUpSet}

+\title{Upset plot of QTL sharing between states with state-level annotations}

+\usage{

+plotUpSet(

+  object,

+  assay = "significant",

+  name = "colnames",

+  min_shared = 10,

+  min_degree = 2,

+  max_degree = NULL,

+  annotate_by = NULL,

+  comb_order = "comb_size",

+  set_order = order(ss),

+  ...

+)

+}

+\arguments{

+\item{object}{an \code{QTLExperiment} object}

+

+\item{assay}{Name of assay to use to assess significance.}

+

+\item{name}{character specifying the column in colData to use to label rows

+and columns. Default is colnames(qtle).}

+

+\item{min_shared}{minimum number of shared QTL for set to be included.}

+

+\item{min_degree}{minimum degree of sharing for set to be included.}

+

+\item{max_degree}{maximum degree of sharing for set to be included.}

+

+\item{annotate_by}{character or array of characters specifying the

+column(s) in colData to be plotted as annotations.}

+

+\item{comb_order}{characters specifying how sets should be ordered. Options

+include the set size (set_size), combination size (comb_size), degree (deg).}

+

+\item{set_order}{Array specifying order of states.}

+

+\item{...}{further arguments passed to \code{\link[Rtsne]{Rtsne}}}

+}

+\value{

+Returns a \code{ComplexHeatmap} object.

+}

+\description{

+Convenient method to plot an UpSet plot showing the number of QTL that are

+significant in sets of states.

+}

+\examples{

+sim <- qtleSimulate(

+    nstates=10, nfeatures=100, ntests=1000,

+    global=0.2, multi=0.4, unique=0.2, k=2)

+sim <- callSignificance(sim, mode="simple", assay="lfsrs", 

+    thresh=0.0001, second.thresh=0.0002)

+sim_sig <- getSignificant(sim)

+sim_top <- getTopHits(sim_sig, assay="lfsrs", mode="state")

+sim_top <- runPairwiseSharing(sim_top)

+

+plotUpSet(sim_top)

+

+# Upset plot with complex row annotations

+plotUpSet(sim_top, annotate_by = c("nSignificant", "multistateGroup"))

+}