column names autodetection

Author: Veera

R/.#ggman.R

@@ -0,0 +1 @@
+veera@hello908.local.69747

R/.Rhistory

@@ -1,93 +1,3 @@
-get(gwas.sig)
-get(gwas.sig)
-deparse(substitute(gwas.sig))
-ggmanLabel(p1,labelDfm = gwas.sig)
-ggmanLabel(p1,labelDfm = gwas.sig)
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP1")
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP")
-names(gwasSig)
-names(gwas.sig)
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP")
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = "SNP",type="hello")
-temp = data.frame(snp = c("rs88888"))
-temp
-ggmanLabel(p1,temp,snp="snp")
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = "SNP")
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = "SNP")
-library(ggman)
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = "SNP")
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = paste0(CHR,":",BP))
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = "BP")
-p1
-names(p1)
-p1$scales
-p1$mapping
-p1$theme
-p1$facet
-names(p1)
-p1$plot_env
-p1$guides
-ggmanLabel(p1,labelDfm = gwas.sig, snp = "SNP", label = "BP")
-ggmanHighlight(p1,highlights)
-ggmanHighlight(p1,highlights)
-ggmanHighlight(p1,highlights,colour="green")
-ggmanHighlight(p1,highlights,colour="green", size = 0.1)
-ggmanHighlight(p1,highlights,colour="green", size = 0.1)
-is.vector
-a = c(1,2,3)
-a
-is.vector(a)
-b = c("A","B","C")
-b
-is.vector(b)
-class(b)
-class(a)
-ls()
-temp
-ggmanHighlight(p1,highlight = c("rsaaaa"))
-ggmanHighlight(p1,highlight = c("rsaaaa"))
-ggmanHighlight(p1,highlight = c("rsaaaa"))
-ls()
-temp <- gwas.sig[gwas.sig$SNP %in% c("rsaaa"),]
-temp
-nrow(temp)
-ggmanHighlight(p1,highlight = c("rsaaaa"))
-ggmanHighlight(p1,highlights,colour="a"
-)
-ggmanHighlight(p1,highlights,colour="a"
-)
-head (gwas)
-ls()
-ggmanZoom(p1, chromosome = "chr1")
-ggmanZoom(p1, chromosome = "chr1")
-ggmanZoom(p1, chromosome = "1")
-ggmanZoom(p1, chromosome = c(1,2))
-ggmanZoom(p1, chromosome = 1,start.position="a")
-ggmanZoom(p1, chromosome = 1,start.position=1,end.posiiton = "b")
-ggmanZoom(p1, chromosome = 1,start.position=1,end.posiiton = "b")
-head(gwas)
-ggmanZoom(p1, chromosome = 1,start.position=1,end.posiiton = 100)
-ggmanZoom(p1, chromosome = 1,start.position=1,end.posiiton = 100)
-ggmanZoom(p1, chromosome = 1,start.position=1,end.position = 100)
-ggmanZoom(p1, chromosome = 1,start.position=1,end.position = 100)
-p2 = ggmanZoom(p1, chromosome = 1,start.position=1,end.position = 100)
-head(gwas.sig)
-head(gwa)
-head(gwas)
-ggmanHighlight(p2,highlight = c("rs1_0_M","rs1_1","rs1_2"))
-head(gwas.sig)
-head(gwas)
-ggplot(gwas[1:100,], aes(BP,P)) + geom_point()
-library(ggplot2)
-ggplot(gwas[1:100,], aes(BP,P)) + geom_point()
-ggplot(gwas[1:100,], aes(BP,P, colour = as.factor(CHR))) + geom_point()
-p1 = ggplot(gwas[1:100,], aes(BP,P, colour = as.factor(CHR))) + geom_point()
-p1 + ggplot(gwas[1:10,],aes(colour = BP))
-p1 + ggplot(gwas[1:10,],aes(colour = as.factor(BP)))+ geom_point()
-p1 + ggplot(gwas[1:10,],aes(colour = as.factor(BP)))+ geom_point(da)
-p1 + geom_point(data = gwas[1:10,], aes(colour = as.factor(BP)))
-p1 = ggplot(gwas[1:100,], aes(BP,P, fill = as.factor(CHR))) + geom_point()
-p1 = ggplot(gwas[1:100,], aes(BP,P, fill = as.factor(CHR))) + geom_point() + guides(fill = FALSE)
 p1 = ggplot(gwas[1:100,], aes(BP,P, fill = as.factor(CHR))) + geom_point() + guides(fill = FALSE)
 p1 + geom_point(data = gwas[1:10,], aes(colour = as.factor(BP)))
 p1 + geom_point(data = gwas[1:10,], aes(colour = as.factor(BP))) + scale_fill_grey()
@@ -498,3 +408,93 @@ mySession = browserSession("UCSC")
 genome(mySession) = "mm10"
 myrange = GRanges("chr6", IRanges(20400587, 20403336))
 myrange
+pmatch
+a =c("chrom","Chrom","Chromosome","chromosome","CHROMOSOME","CHR")
+grep ("chr",a)
+grep ("chr",a, ignore.case=TRUE)
+grep ("chrom",a, ignore.case=TRUE)
+grep ("\bchrom",a, ignore.case=TRUE)
+grep ("\\bchrom",a, ignore.case=TRUE)
+grep ("\\bchrom\\b",a, ignore.case=TRUE)
+ls()
+dfmnames <- c("CHR","SNP","P","BP")
+search.names("chr")
+search.names("chr")
+search.names("snp")
+search.names("bp")
+search.names("p")
+search.names("p")
+search.names("p")
+dfmnames <- c("CHromosome","BP","Snp","Pvalue")
+search.names("p")
+search.names(c("p","pvalue"))
+search.names(c("pvalue","p"))
+search.names(c("pvalue","p","pvalue"))
+search.names(c("pvalue","p","pvalue"))
+search.names(c("chr"))
+search.names(c("chr","chrom"))
+search.names(c("chr","chrom","chromosome"))
+search.names("bp")
+dfmnames <- c("CHromosome","Base Pair","Snp","Pvalue")
+search.names("bp")
+search.names("base")
+search.names("basepair")
+dfmnames <- c("CHromosome","Base_pair","Snp","Pvalue")
+search.names("basepair")
+library(ggman)
+search.dfm.names(toy)
+dfmnames <- names(toy.gwas)
+search.dfm.names(toy.gwas)
+temp = search.dfm.names(toy.gwas)
+names(temp)
+temp = search.dfm.names(toy.gwas)
+temp
+names(temp)
+temp = search.dfm.names(toy.gwas)
+temp
+dfm.names <- c("bp","BP","basepair")
+dfmnames <- c("bp","BP","basepair")
+search.names("bp")
+dfmnames <- c("bp")
+search.names("bp")
+dfmnames <- c("bp","BP")
+search.names("bp")
+temp
+names(toy.gwas)
+names(toy.gwas)[1] <- "marker"
+names(toy.gwas)
+search.dfm.names(toy.gwas)
+dfmnames <- c("bp","BP")
+search.names("bp")
+temp = search.names("bp")
+class(temp)
+is.null(temp)
+search.dfm.names(toy.gwas)
+temp = search.dfm.names(toy.gwas)
+grep(NA,temp)
+grep("NA",temp)
+is.na(temp)
+which(is.na(temp))
+which(is.na(temp))
+names(temp)[which(is.na(temp))]
+names(toy.gwas)
+names(toy.gwas)[2] <- "brom"
+temp = search.dfm.names(toy.gwas)
+temp
+names(toy.gwas)[2] <- "brom"
+names(temp)[which(is.na(temp))]
+temp = names(temp)[which(is.na(temp))]
+paste(temp)
+ls()
+temp
+temp = search.dfm.names(toy.gwas)
+temp
+temp$bp
+temp["bp"]
+head(toy.gwas[,temp["bp"]])
+library(ggman)
+ggman(toy,gwas)
+ggman(toy,gwas)
+search.names()
+ggman(toy,gwas)
+ggman(toy.gwas)

R/check.input.ggman.R

@@ -26,37 +26,46 @@ check.input.ggman <- function(){
     if(!any(class(gwas) == "data.frame")){
         stop("The gwas input is not a data frame")
     }
-    ## snp input
-    if(class(snp) != "character"){
-        stop("The snp input is not a character")
-    }
-    if(!snp %in% names(gwas)){
-        stop(paste0("The column \'",snp,"\' is not present in the input data frame"))
-    }
-    ## bp input
-    if(class(bp) != "character"){
-        stop("The bp input is not a character")
-    }
-    if(! bp %in% names(gwas)){
-        stop(paste0("The column \'",bp,"\' is not present in the input data frame"))
-    }
 
-    ##chrom input
-    if(class(chrom) != "character"){
-        stop("The chrom input is not a character")
-    }
-    if(! chrom %in% names(gwas)){
-        stop(paste0("The column \'",chrom,"\' is not present in the input data frame"))
-    }
+    dfmnames <- names(gwas)
 
-    ## pvalue input
-    if(class(pvalue) != "character"){
-        stop("The pvalue input is not a character")
-    }
-    if(! pvalue %in% names(gwas)){
-        stop(paste0("The column \'",pvalue,"\' is not present in the input data frame"))
-    }
+        ##chrom input
+        if(class(chrom) != "character"){
+            stop("The chrom input is not a character")
+        }
+        if(! chrom %in% names(gwas)){
+            stop(paste0("The column \'",chrom,"\' is not present in the input data frame"))
+        }
+
+
+
+        if(class(snp) != "character"){
+            stop("The snp input is not a character")
+        }
+        if(!snp %in% names(gwas)){
+            stop(paste0("The column \'",snp,"\' is not present in the input data frame"))
+        }
+    
+
+
+        ## bp input
+        if(class(bp) != "character"){
+            stop("The bp input is not a character")
+        }
+        if(! bp %in% names(gwas)){
+            stop(paste0("The column \'",bp,"\' is not present in the input data frame"))
+        }
+
+
+        ## pvalue input
+        if(class(pvalue) != "character"){
+            stop("The pvalue input is not a character")
+        }
+        if(! pvalue %in% names(gwas)){
+            stop(paste0("The column \'",pvalue,"\' is not present in the input data frame"))
+        }
 
+   
     ## sigline input
     if(!is.na(sigLine)){
         if(!is.numeric(sigLine)){

R/ggman.R

@@ -78,7 +78,7 @@ utils::globalVariables(c("index","marker","chrom_alt","group","xbreaks"))
 #' @export
 ggman <- function(gwas,
                   clumps = NA,
-                  snp = "snp", bp = "bp", chrom = "chrom", pvalue = "pvalue",
+                  snp = NA, bp = NA, chrom = NA, pvalue = NA,
                   sigLine = 8,
                   lineColour = "red",
                   pointSize = 0.1,
@@ -91,9 +91,45 @@ ggman <- function(gwas,
 
     ##define global variables to escape R CMD check
 
-    ##check the inputs    
+
+    dfmnames <- names(gwas)
+        ## chrom input
+    if(is.na(chrom)){
+        chrom <- search.names(c("chr","chrom","chromosome"), dfmnames)
+        if(is.null(chrom)){
+            stop("Couldn't find the chromosome column.
+Specify the name of the column with chromosome ids")
+        }
+    }
+
+        if(is.na(snp)){
+        snp <- search.names(c("snp","rsid"), dfmnames)
+        if(is.null(snp)){
+            stop("Couldn't find the snp column.
+Specify the name of the column with snp ids")
+        }
+        }
+
+        if(is.na(bp)){
+        bp <- search.names(c("bp","basepair","position","start"),dfmnames)
+        if(is.null(bp)){
+            stop("Couldn't find the bp column.
+Specify the name of the column with bp ids")
+        }
+        }
+        if(is.na(pvalue)){
+        pvalue <- search.names(c("p","pval","pvalue"), dfmnames)
+        if(is.null(pvalue)){
+            stop("Couldn't find the pvalue column.
+Specify the name of the column with pvalues")
+        }
+        }
+
+    
+    ##check the inputs
     environment(check.input.ggman) <- environment()
     check.input.ggman()
+
     dfm <- as.data.frame(gwas)
     dfm$chrom <- dfm[,chrom]
     dfm$bp <- as.numeric(as.character(dfm[,bp]))

R/search.dfm.names.R

@@ -0,0 +1,20 @@
+
+#' search.names
+#'
+#' @keywords internal
+#'
+#' @return Nothing; internal function
+#' 
+search.names <- function(term,dfmnames){
+    for(i in 1:length(term)){
+        res <- grep(paste0("\\b",term[i],"\\b"),dfmnames, ignore.case = TRUE)
+        if(length(res)>0){
+            if(length(res)==1){
+                return(dfmnames[res])
+            }
+        }
+    }
+}
+    
+
+