ggmanZoom_addpoints

Author: drveera

.Rhistory

@@ -245,3 +245,104 @@ q()
 n
 q()
 n
+head(p2$data)
+dfm0 <- p2$data
+dfm0
+dfm1 <- toy.gwas
+library(data.table)
+dfm <- toy.gwas
+head(dfm0)
+dfm <- toy.gwas[1:20]
+dfm <- toy.gwas[1:20,]
+dfm
+snp="snp"
+head(toy.gwas)
+head(dfm1)
+head(dfm0)
+head(dfm1)
+head(dfm)
+dfm <- toy.gwas 
+head(dfm)
+head(dfm1)
+dfm
+dfm1 <- data.frame(snp="rs1_3595",pvalue=0.80)
+dfm1
+dfm
+head(dfm0)
+dim(dfm0)
+dfm <- dfm[,c("snp","pvalue")]
+dfm
+dfm0
+dfm
+dfm <- dfm0
+dfm
+dfm$pvalue <- dfm$pvalue-0.1
+dfm
+dfm[3,2]
+dfm[3,3]
+dfm[2,3]
+dfm[2,3] <- 0.05
+dfm
+p1
+head(dfm0)
+p1
+dfm
+p1
+dfm0
+head(dfm0)
+head(dfm)
+ggmanZoomPlot
+p1
+d1$c
+1:10
+length(d1)
+dim(d1)
+d1
+d1
+d2
+p1
+head(dfm)
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+p1
+ggave("test.pdf")
+ggsave("test.pdf")
+system("open test.pdf")
+class(ggmanZoomPlot)
+color="red"
+color.legend.title="Analysis"
+color.legend.name="new analysis"
+scm
+p1
+scm
+p1
+getwd()
+q()
+n
+q()
+n
+class(ggmanZoomPlot)
+a = list(a=1,b=2)
+a
+a$a
+a$b
+q()
+n
+x
+(
+q()
+n
+head(tempdfm)
+tempdfm
+tempdfm
+?q

NAMESPACE

@@ -7,6 +7,7 @@ export(ggmanHighlightGroup)
 export(ggmanLabel)
 export(ggmanZoom)
 export(ggmanZoom.old)
+export(ggmanZoom_addpoints)
 import(ggplot2)
 import(ggrepel)
 importFrom(gtools,mixedorder)

R/.#ggmanZoom.R

@@ -0,0 +1 @@
+veera@Veeras-MacBook-Pro-2.local.3651

R/genetracks.refseq.R

@@ -124,5 +124,17 @@ genetracks.refseq <- function(){
                                                 ymax = ymax, fill = as.factor(strand)),
                           alpha = 0.03,inherit.aes = FALSE) 
     }
-    p1 + scale_y_continuous(breaks = 0:ymax+1, labels = 0:ymax+1, limits = c(-1-(as.numeric(stack.level)), ymax)) 
+    p1 + scale_y_continuous(breaks = 0:ymax+1, labels = 0:ymax+1, limits = c(-1-(as.numeric(stack.level)), ymax))
+    if(!is.na(point.legend.title)){
+      scm = c(point.color)
+      names(scm) = point.legend.name
+      p1 <- p1 + geom_point(aes(color=point.legend.name))+
+        scale_color_manual(name=point.legend.title,
+                           values=scm)
+    }
+    class(p1) <- append(class(p1),"ggman")
+    p1 <- list(plot=p1,
+               point.legend.title=point.legend.title,
+               scm=scm)
+    return(p1)
 }

R/ggman.R

@@ -251,5 +251,4 @@ Specify the name of the column with pvalues")
         class(p1) <- append(class(p1), "ggman")
         return(p1)
     }
-    
 }

R/ggmanZoom.R

@@ -18,6 +18,8 @@
 #' @param xlabel X axis label 
 #' @param ylabel Y axis label
 #' @param title Plot title
+#' @param point.legend.title point legend title
+#' @param point.legend.name point legend name
 #' @param ... other arguments to pass to \code{\link{geom_point}}
 #' @return A regional association plot 
 #' 
@@ -54,6 +56,9 @@ ggmanZoom <- function(
                       xlabel = NA,
                       ylabel = NA,
                       title = NA,
+                      point.legend.title=NA,
+                      point.legend.name=NA,
+                      point.color="black",
                       ...
                       ){
     ##check inputs
@@ -83,13 +88,17 @@ ggmanZoom <- function(
     }
 
     p1 <- ggplot(dfm.sub, aes(bp,marker)) + geom_point(...) +
-        labs(x = xlabel, y = ylabel, title = title)    
-
+        labs(x = xlabel, y = ylabel, title = title)
     if(gene.tracks){
         ##refseq
         environment(genetracks.refseq) <- environment()
         genetracks.refseq()
     } else {
+      scm = c(point.color)
+      names(scm) = point.legend.name
+      p1 <- list(plot=p1,
+                 scm.title = point.legend.title,
+                 scm = scm)
         return(p1)
     }
 }

R/ggmanZoom_addpoints.R

@@ -0,0 +1,48 @@
+#' ggmanZoom_addpoints
+#'
+#' Zoom in to a specific region of the Manhattan Plot
+#'
+#' @param ggmanPlot A ggplot object of class 'ggman'
+#' @param chromosome Chromosome identifier
+#' @param start.position Starting basepair position
+#' @param end.position Ending basepair position
+#' @param ... other arguments to pass to \code{\link{geom_point}}
+#' @return A regional association plot 
+#'
+#' @examples
+#'
+#'
+#'
+#'
+#'
+#'
+#' @export
+ggmanZoom_addpoints <- function(ggmanZoomPlot,
+                                dfm,
+                                snp="SNP",
+                                pvalue="P",
+                                point.color = "red",
+                                point.legend.name="new analysis",
+                                ...){
+  ggmanZoomPlot1 <- ggmanZoomPlot[[1]]
+  dfm0 <- ggmanZoomPlot1$data
+  dfm <- as.data.frame(dfm)
+  dfm1 <- data.frame(snp = dfm[,snp],pvalue=dfm[,"pvalue"])
+  dfm <- merge(dfm0[,c("snp","index","bp")],dfm1,by="snp")
+  dfm$marker <- -log10(dfm$pvalue)
+  scmnames <- c(names(ggmanZoomPlot$scm),point.legend.name)
+  scm <- c(ggmanZoomPlot$scm,point.color)
+  names(scm) <- scmnames
+  point.legend.title <- ggmanZoomPlot$point.legend.title
+  p1 <- ggmanZoomPlot1 +
+    geom_point(data=dfm,aes(color=point.legend.name), shape=5)+
+    scale_color_manual(name=point.legend.title,
+                       values=scm)
+  class(p1) <- append(class(p1), "ggman")
+  p1 <- list(plot=p1,
+             scm=scm,
+             point.legend.title=point.legend.title)
+  return(p1)
+
+
+}