Merge pull request #2 from kevinrue/master

VioFun supports ylim argument

Author: lengning

.gitignore

@@ -0,0 +1,6 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+*.tar.gz
+*.Rd

SCPattern.Rproj

@@ -0,0 +1,22 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 4
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+StripTrailingWhitespace: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackagePath: package/SCPattern
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

package/SCPattern/DESCRIPTION

@@ -1,16 +1,19 @@
 Package: SCPattern
 Type: Package
 Title: SCPattern : single cell RNA-seq multiple condition analysis 
-Version: 0.0.4
-Date: 2015-12-15
-Author: Ning Leng
-Maintainer: Ning Leng <lengning1@gmail.com>
+Version: 0.0.5
+Date: 2017-03-19
+Authors@R: c(
+    person("Ning", "Leng", role = c("aut", "cre"),
+        email = "lengning1@gmail.com"),
+    person(given="Kevin", family="Rue-Albrecht", role = c("ctb"))
+    )
 Depends: EBSeq, testthat, vioplot, gtools, DirichletReg
 Suggests: VGAM
 Description: SCPattern is a statistical method that classify genes into expression patterns in a multiple condition single cell RNA-seq experiment.
 License: Artistic-2.0
 LazyLoad: yes
-Collate:'BetaempH0.R'
+Collate: 'BetaempH0.R'
   'DirichletempH0.R'
   'KSDir.R'
   'KSNoDir.R'
@@ -22,3 +25,4 @@ Collate:'BetaempH0.R'
   'DirichletOptim.R'
 BuildVignettes: no
 biocViews: StatisticalMethod, RNASeq, Sequencing, GeneExpression
+RoxygenNote: 6.0.1

package/SCPattern/R/VioFun.R

@@ -1,26 +1,30 @@
 #' @title Plot violinplot
-#' @usage VioFun(gene, Data, Conditions, Col, main_pre=NULL, Dropout.remove=FALSE, Dropout.upper=0, namecex=1, ylab="Expression", Log="")
+#' @usage VioFun(
+#'   gene, Data, Conditions, Col, main_pre=NULL, Dropout.remove=FALSE,
+#'   Dropout.upper=0, namecex=1, ylab="Expression", Log="", ...)
 #' @param gene gene name of interest (character)
 #' @param Data input data, gene-by-sample matrix. Normalized expression is expected
 #' @param Conditions a vector of characters that indicates which condition the cells belong to
 #' @param Col colors
 #' @param main_pre prefix for main
-#' @param namecex cex for x axis names 
+#' @param namecex cex for x axis names
 #' @param ylab y axis label
 #' @param Log whether plot in log scale
-#' @param Droupout.remove,Dropout.upper For a given gene, whether cells with dropout will be 
+#' @param Droupout.remove,Dropout.upper For a given gene, whether cells with dropout will be
 #' ignored in the test. Defaulte is FALSE. If it is set to TRUE, values that are less or equal to
 #' Dropout.upper will be ignored during the test.
-#' @return violin plot 
+#' @param ... additional arguments passed on to methods (e.g., ylim for vioplot).
+#' @return violin plot
 #' @examples Data<- abs(matrix(rnorm(20,100,2), nrow=2))
 #' rownames(Data) <- paste0("gene",1:2)
 #' cond <- factor(rep(c("a","b"),each=5))
 #' VioFun("gene1",Data, cond)
 #' @author Ning Leng
 
-VioFun=function(gene, Data, Conditions, Col=NULL, main_pre=NULL, 
+VioFun=function(gene, Data, Conditions, Col=NULL, main_pre=NULL,
 			Dropout.remove=FALSE, Dropout.upper=0, namecex=1,
-			ylab="Expression", Log=""){
+			ylab="Expression", Log="", ...){
+    dots <- list(...)
 	SCMat <- Data
 	SCCond <- Conditions
 	if(!is.factor(SCCond))SCCond <- factor(SCCond, levels=unique(SCCond))
@@ -39,15 +43,27 @@ VioFun=function(gene, Data, Conditions, Col=NULL, main_pre=NULL,
   names(SCDataVio) <- paste0(levels(SCCond)," (",sapply(SCDataVio,length),")")
 
   tmpmin <- 0
-  if(Log=="y")tmpmin <- 1
-  plot(1,1,col="white",xlim=c(0,length(SCDataVio)+1),
-  ylim=c(tmpmin,(max(SCMat[gene,])+.1)*1.2),
-  xaxt="none",ylab=ylab, xlab="",main=paste(gene, mainpaste),
-  log=Log)
+  if (Log=="y"){
+      tmpmin <- 1
+  }
+  if ("ylim" %in% names(dots)){
+      ylim <- dots[["ylim"]]
+  } else {
+      ylim=c(tmpmin,(max(SCMat[gene,])+.1)*1.2)
+  }
+  plot(
+      1,1,col="white",xlim=c(0,length(SCDataVio)+1),
+      ylim = ylim,
+      xaxt="none",ylab=ylab, xlab="",main=paste(gene, mainpaste),
+      log=Log
+    )
   mtext(side=1,at=1:length(SCDataVio),paste0(names(SCDataVio)," "),
 las=3,cex=namecex)
-  for(j in 1:length(SCDataVio))
-  if(max(SCDataVio[[j]])>0)vioplot(SCDataVio[[j]],at=j, add=T,col=Col[j],colMed=NULL)
+  for(j in 1:length(SCDataVio)){
+      if(max(SCDataVio[[j]])>0){
+          vioplot(SCDataVio[[j]],at=j, add=T,col=Col[j],colMed=NULL)
+      }
+  }
 }