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| ##################################################### | |
| ## (A) Add fingerprint folding argument to desc2fp ## | |
| ########################################## | |
| ## Intersect and Venn Diagram Functions ## | |
| ########################################## | |
| ## Author: Thomas Girke | |
| ## Last update: March 24, 2012 | |
| ## Utilities: | |
| ## (1) Venn Intersects | |
| ## Computation of Venn intersects among 2-20 or more sample sets using the typical | |
| ## 'only in' intersect logic of Venn comparisons, such as: objects present only in | |
| ## set A, objects present only in the intersect of A & B, etc. Due to this restrictive | |
| ## intersect logic, the combined Venn sets contain no duplicates. | |
| ## (2) Regular Intersects | |
| ## Computation of regular intersects among 2-20 or more sample sets using the | |
| ## following intersect logic: objects present in the intersect of A & B, objects present | |
| ## in the intersect of A & B & C, etc. The approach results usually in many duplications | |
| ## of objects among the intersect sets. | |
| ## (3) Graphical Utilities | |
| ## - Venn diagrams of 2-5 sample sets. | |
| ## - Bar plots for the results of Venn intersect and all intersect approaches derived | |
| ## from many samples sets. | |
| ## | |
| ## Detailed instructions for using the functions of this script are available on this page: | |
| ## http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_graphics_venn | |
| ## | |
| ## Revision history: | |
| ## March 24, 2012: fixed substring problem in plotVenn function | |
| ####################################### | |
| ## Define Generic Intersect Function ## | |
| ####################################### | |
| ## Computation of (1) Venn Intersects and (2) Regular Intersects | |
| overLapper <- function(setlist=setlist, complexity=1:length(setlist), sep="-", cleanup=FALSE, keepdups=FALSE, type) { | |
| ## Clean up of sample sets to minimize formatting issues | |
| if(cleanup==TRUE) { | |
| ## Set all characters to upper case | |
| setlist <- sapply(setlist, function(x) gsub("([A-Z])", "\\U\\1", x, perl=T, ignore.case=T)) | |
| ## Remove leading and trailing spaces | |
| setlist <- sapply(setlist, function(x) gsub("^ {1,}| {1,}$", "", x, perl=T, ignore.case=T)) | |
| } | |
| ## Append object counter to retain duplicates | |
| if(keepdups==TRUE) { | |
| dupCount <- function(setlist=setlist) { | |
| count <- table(setlist) | |
| paste(rep(names(count), count), unlist(sapply(count, function(x) seq(1, x))), sep=".") | |
| } | |
| mynames <- names(setlist) | |
| setlist <- lapply(setlist, function(x) dupCount(x)) # lapply necessary for numeric data! | |
| names(setlist) <- mynames | |
| } | |
| ## Create intersect matrix (removes duplicates!) | |
| setunion <- sort(unique(unlist(setlist))) | |
| setmatrix <- sapply(names(setlist), function(x) setunion %in% unique(setlist[[x]])) | |
| rownames(setmatrix) <- setunion | |
| storage.mode(setmatrix) <- "numeric" | |
| ## Create all possible sample combinations within requested complexity levels | |
| labels <- names(setlist) | |
| allcombl <- lapply(complexity, function(x) combn(labels, m=x, simplify=FALSE)) | |
| allcombl <- unlist(allcombl, recursive=FALSE) | |
| complevels <- sapply(allcombl, length) | |
| ## Return intersect list for generated sample combinations | |
| if(type=="intersects") { | |
| OLlist <- sapply(seq(along=allcombl), function(x) setunion[rowSums(setmatrix[, rep(allcombl[[x]], 2)]) == 2 * length(allcombl[[x]])]) | |
| names(OLlist) <- sapply(allcombl, paste, collapse=sep) | |
| return(list(Set_List=setlist, Intersect_Matrix=setmatrix, Complexity_Levels=complevels, Intersect_List=OLlist)) | |
| } | |
| ## Return Venn intersect list for generated sample combinations | |
| if(type=="vennsets") { | |
| vennSets <- function(setmatrix=setmatrix, allcombl=allcombl, index=1) { | |
| mycol1 <- which(colnames(setmatrix) %in% allcombl[[index]]) | |
| mycol2 <- which(!colnames(setmatrix) %in% allcombl[[index]]) | |
| cond1 <- rowSums(setmatrix[, rep(mycol1, 2)]) == 2 * length(mycol1) | |
| cond2 <- rowSums(setmatrix[, rep(mycol2, 2)]) == 0 | |
| return(setunion[cond1 & cond2]) | |
| } | |
| vennOLlist <- sapply(seq(along=allcombl), function(x) vennSets(setmatrix=setmatrix, allcombl=allcombl, index=x)) | |
| names(vennOLlist) <- sapply(allcombl, paste, collapse=sep) | |
| return(list(Set_List=setlist, Intersect_Matrix=setmatrix, Complexity_Levels=complevels, Venn_List=vennOLlist)) | |
| } | |
| } | |
| ########################################### | |
| ## Define Venn Diagram Plotting Function ## | |
| ########################################### | |
| vennPlot <- function(counts=counts, mymain="Venn Diagram", mysub="default", setlabels="default", yoffset=seq(0,10,by=0.34), ccol=rep(1,31), colmode=1, lcol=c("#FF0000", "#008B00", "#0000FF", "#FF00FF", "#CD8500"), lines=c("#FF0000", "#008B00", "#0000FF", "#FF00FF", "#CD8500"), mylwd=3, diacol=1, type="ellipse", ccex=1.0, lcex=1.0, sepsplit="_", ...) { | |
| ## Enforce list structure to support multiple venn sets | |
| if(is.list(counts)==FALSE) { | |
| counts <- list(counts) | |
| } | |
| ## Check for supported number of Venn counts: 3, 7, 15 and 31 | |
| if(!length(counts[[1]]) %in% c(3,7,15,31)) stop("Only the counts from 2-5 way venn comparisons are supported.") | |
| ## Function to return for a set label the index of matches in the name field of a counts object | |
| grepLabel <- function(label, x=names(counts[[1]])) { | |
| x <- strsplit(x, sepsplit) | |
| as.numeric(which(sapply(x, function(y) any(y==label)))) | |
| } | |
| ## 2-way Venn diagram | |
| if(length(counts[[1]])==3) { | |
| ## Define subtitle | |
| if(mysub=="default") { | |
| n <- names(counts[[1]])[1:2] | |
| if(!all(rowSums(sapply(n, function(x) sapply(n, function(y) grepl(y, x)))) == 1)) { # Checks if one or more set labels are substrings of one another | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| if(sum(grepl(sepsplit, n)) > 0 | !all(grepl(sepsplit, names(counts[[1]][-c(1:length(n))])))) { sample_counts <- rep("?", length(n)); warning("Set labels are substrings of one another. To fix this, the set labels need to be separated by character provided under \"sepsplit\", but the individual names cannot contain this character themselves.") } | |
| } else { | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grep(x, names(counts[[1]]))])) | |
| } | |
| mysub <- paste(paste("Unique objects: All =", sum(counts[[1]])), paste("; S1 =", sample_counts[1]), paste("; S2 =", sample_counts[2]), sep="") | |
| } else { | |
| mysub <- mysub | |
| } | |
| ## Plot venn shapes | |
| symbols(x=c(4, 6), y = c(6, 6), circles=c(2, 2), xlim=c(0, 10), ylim=c(0, 10), inches=F, main=mymain, sub=mysub, lwd=mylwd, xlab="", ylab="", xaxt="n", yaxt="n", bty="n", fg=lines, ...); | |
| ## Add counts | |
| for(i in seq(along=counts)) { | |
| olDF <- data.frame(x=c(3.1, 7.0, 5.0), | |
| y=c(6.0, 6.0, 6.0), | |
| counts=counts[[i]]) | |
| if(colmode==1) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol, cex=ccex, ...) } | |
| if(colmode==2) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol[[i]], cex=ccex[i], ...) } # For coloring several numbers per intersect differently. ccol can needs to be list to color each field differently.. | |
| } | |
| ## Add sample labels | |
| if(length(setlabels)==1 & setlabels[1]=="default") { | |
| setlabels <- names(counts[[1]][1:2]) | |
| } else { | |
| setlabels <- setlabels | |
| } | |
| text(c(2.0, 8.0), c(8.8, 8.8), labels=setlabels, col=lcol, cex=lcex, ...) | |
| } | |
| ## 3-way Venn diagram | |
| if(length(counts[[1]])==7) { | |
| ## Define subtitle | |
| if(mysub=="default") { | |
| n <- names(counts[[1]])[1:3] | |
| if(!all(rowSums(sapply(n, function(x) sapply(n, function(y) grepl(y, x)))) == 1)) { # Checks if one or more set labels are substrings of one another | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| if(sum(grepl(sepsplit, n)) > 0 | !all(grepl(sepsplit, names(counts[[1]][-c(1:length(n))])))) { sample_counts <- rep("?", length(n)); warning("Set labels are substrings of one another. To fix this, the set labels need to be separated by character provided under \"sepsplit\", but the individual names cannot contain this character themselves.") } | |
| } else { | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| } | |
| mysub <- paste(paste("Unique objects: All =", sum(counts[[1]])), paste("; S1 =", sample_counts[1]), paste("; S2 =", sample_counts[2]), paste("; S3 =", sample_counts[3]), sep="") | |
| } else { | |
| mysub <- mysub | |
| } | |
| ## Plot venn shapes | |
| symbols(x=c(4, 6, 5), y=c(6, 6, 4), circles=c(2, 2, 2), xlim=c(0, 10), ylim=c(0, 10), inches=FALSE, main=mymain, sub=mysub, lwd=mylwd, xlab="", ylab="", xaxt="n", yaxt="n", bty="n", fg=lines, ...) | |
| ## Add counts | |
| for(i in seq(along=counts)) { | |
| olDF <- data.frame(x=c(3.0, 7.0, 5.0, 5.0, 3.8, 6.3, 5.0), | |
| y=c(6.5, 6.5, 3.0, 7.0, 4.6, 4.6, 5.3), | |
| counts=counts[[i]]) | |
| if(colmode==1) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol, cex=ccex, ...) } | |
| if(colmode==2) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol[[i]], cex=ccex[i], ...) } | |
| } | |
| ## Add sample labels | |
| if(length(setlabels)==1 & setlabels[1]=="default") { | |
| setlabels <- names(counts[[1]][1:3]) | |
| } else { | |
| setlabels <- setlabels | |
| } | |
| text(c(2.0, 8.0, 6.0), c(8.8, 8.8, 1.1), labels=setlabels, col=lcol, cex=lcex, ...) | |
| } | |
| ## 4-way Venn diagram with ellipses | |
| if(length(counts[[1]])==15 & type=="ellipse") { | |
| ## Define subtitle | |
| if(mysub=="default") { | |
| n <- names(counts[[1]])[1:4] | |
| if(!all(rowSums(sapply(n, function(x) sapply(n, function(y) grepl(y, x)))) == 1)) { # Checks if one or more set labels are substrings of one another | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| if(sum(grepl(sepsplit, n)) > 0 | !all(grepl(sepsplit, names(counts[[1]][-c(1:length(n))])))) { sample_counts <- rep("?", length(n)); warning("Set labels are substrings of one another. To fix this, the set labels need to be separated by character provided under \"sepsplit\", but the individual names cannot contain this character themselves.") } | |
| } else { | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| } | |
| mysub <- paste(paste("Unique objects: All =", sum(counts[[1]])), paste("; S1 =", sample_counts[1]), paste("; S2 =", sample_counts[2]), paste("; S3 =", sample_counts[3]), paste("; S4 =", sample_counts[4]), sep="") | |
| } else { | |
| mysub <- mysub | |
| } | |
| ## Plot ellipse | |
| plotellipse <- function (center=c(1,1), radius=c(1,2), rotate=1, segments=360, xlab="", ylab="", ...) { | |
| angles <- (0:segments) * 2 * pi/segments | |
| rotate <- rotate*pi/180 | |
| ellipse <- cbind(radius[1] * cos(angles), radius[2] * sin(angles)) | |
| ellipse <- cbind( ellipse[,1]*cos(rotate) + ellipse[,2]*sin(rotate), ellipse[,2]*cos(rotate) - ellipse[,1]*sin(rotate) ) | |
| ellipse <- cbind(center[1]+ellipse[,1], center[2]+ellipse[,2]) | |
| plot(ellipse, type = "l", xlim = c(0, 10), ylim = c(0, 10), xlab = "", ylab = "", ...) | |
| } | |
| ## Plot ellipse as 4-way venn diagram | |
| ellipseVenn <- function(...) { | |
| split.screen(c(1,1)) | |
| plotellipse(center=c(3.5,3.6), radius=c(2,4), rotate=-35, segments=360, xlab="", ylab="", col=lines[1], axes=FALSE, main=mymain, sub=mysub, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(4.7,4.4), radius=c(2,4), rotate=-35, segments=360, xlab="", ylab="", col=lines[2], axes=FALSE, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(5.3,4.4), radius=c(2,4), rotate=35, segments=360, xlab="", ylab="", col=lines[3], axes=FALSE, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(6.5,3.6), radius=c(2,4), rotate=35, segments=360, xlab="", ylab="", col=lines[4], axes=FALSE, lwd=mylwd, ...) | |
| ## Add counts | |
| for(i in seq(along=counts)) { | |
| olDF <- data.frame(x=c(1.5, 3.5, 6.5, 8.5, 2.9, 3.1, 5.0, 5.0, 6.9, 7.1, 3.6, 5.8, 4.2, 6.4, 5.0), | |
| y=c(4.8, 7.2, 7.2, 4.8, 5.9, 2.2, 0.7, 6.0, 2.2, 5.9, 4.0, 1.4, 1.4, 4.0, 2.8), | |
| counts=counts[[i]]) | |
| if(colmode==1) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol, cex=ccex, ...) } | |
| if(colmode==2) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol[[i]], cex=ccex[i], ...) } | |
| } | |
| ## Add sample labels | |
| if(length(setlabels)==1 & setlabels[1]=="default") { | |
| setlabels <- names(counts[[1]][1:4]) | |
| } else { | |
| setlabels <- setlabels | |
| } | |
| text(c(0.4, 2.8, 7.5, 9.4), c(7.3, 8.3, 8.3, 7.3), labels=setlabels, col=lcol, cex=lcex, ...) | |
| close.screen(all=TRUE) | |
| } | |
| ellipseVenn(...) | |
| } | |
| ## 4-way Venn diagram with circles (pseudo-venn diagram that misses two overlap sectors) | |
| if(length(counts[[1]])==15 & type=="circle") { | |
| ## Define subtitle | |
| if(mysub=="default") { | |
| n <- names(counts[[1]])[1:4] | |
| if(!all(rowSums(sapply(n, function(x) sapply(n, function(y) grepl(y, x)))) == 1)) { # Checks if one or more set labels are substrings of one another | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| if(sum(grepl(sepsplit, n)) > 0 | !all(grepl(sepsplit, names(counts[[1]][-c(1:length(n))])))) { sample_counts <- rep("?", length(n)); warning("Set labels are substrings of one another. To fix this, the set labels need to be separated by character provided under \"sepsplit\", but the individual names cannot contain this character themselves.") } | |
| } else { | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| } | |
| mysub <- paste(paste("Unique objects: All =", sum(counts[[1]])), paste("; S1 =", sample_counts[1]), paste("; S2 =", sample_counts[2]), paste("; S3 =", sample_counts[3]), paste("; S4 =", sample_counts[4]), sep="") | |
| } else { | |
| mysub <- mysub | |
| } | |
| ## Plot venn shapes | |
| symbols(x=c(4, 5.5, 4, 5.5), y = c(6, 6, 4.5, 4.5), circles=c(2, 2, 2, 2), xlim=c(0, 10), ylim=c(0, 10), inches=FALSE, main=mymain, sub=mysub, lwd=mylwd, xlab="", ylab="", xaxt="n", yaxt="n", bty="n", fg=lines, ...) | |
| ## Add counts | |
| for(i in seq(along=counts)) { | |
| olDF <- data.frame(x=c(3.0, 6.5, 3.0, 6.5, 4.8, 3.0, 4.8, 4.8, 6.5, 4.8, 3.9, 5.7, 3.9, 5.7, 4.8), | |
| y=c(7.2, 7.2, 3.2, 3.2, 7.2, 5.2, 0.4, 0.4, 5.2, 3.2, 6.3, 6.3, 4.2, 4.2, 5.2), | |
| counts=counts[[i]]) | |
| if(colmode==1) { text(olDF$x[-c(7,8)], olDF$y[-c(7,8)] + yoffset[i], olDF$counts[-c(7,8)], col=ccol, cex=ccex, ...) } # rows 14-15 of olDF are printed in next step | |
| if(colmode==2) { text(olDF$x[-c(7,8)], olDF$y[-c(7,8)] + yoffset[i], olDF$counts[-c(7,8)], col=ccol[[i]], cex=ccex[i], ...) } | |
| text(c(4.8), c(0.8) + yoffset[i], paste("Only in ", names(counts[[1]][1]), " & ", names(counts[[1]][4]), ": ", olDF$counts[7], "; Only in ", names(counts[[1]][2]), " & ", names(counts[[1]][3]), ": ", olDF$counts[8], sep=""), col=diacol, cex=ccex, ...) | |
| } | |
| ## Add sample labels | |
| if(length(setlabels)==1 & setlabels[1]=="default") { | |
| setlabels <- names(counts[[1]][1:4]) | |
| } else { | |
| setlabels <- setlabels | |
| } | |
| text(c(2.0, 7.5, 2.0, 7.5), c(8.3, 8.3, 2.0, 2.0), labels=setlabels, col=lcol, cex=lcex, ...) | |
| } | |
| ## 5-way Venn diagram | |
| if(length(counts[[1]])==31) { | |
| ## Define subtitle | |
| if(mysub=="default") { | |
| n <- names(counts[[1]])[1:5] | |
| if(!all(rowSums(sapply(n, function(x) sapply(n, function(y) grepl(y, x)))) == 1)) { # Checks if one or more set labels are substrings of one another | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| if(sum(grepl(sepsplit, n)) > 0 | !all(grepl(sepsplit, names(counts[[1]][-c(1:length(n))])))) { sample_counts <- rep("?", length(n)); warning("Set labels are substrings of one another. To fix this, the set labels need to be separated by character provided under \"sepsplit\", but the individual names cannot contain this character themselves.") } | |
| } else { | |
| sample_counts <- sapply(n, function(x) sum(counts[[1]][grepLabel(x, names(counts[[1]]))])) | |
| } | |
| mysub <- paste(paste("Unique objects: All =", sum(counts[[1]])), paste("; S1 =", sample_counts[1]), paste("; S2 =", sample_counts[2]), paste("; S3 =", sample_counts[3]), paste("; S4 =", sample_counts[4]), paste("; S5 =", sample_counts[5]), sep="") | |
| } else { | |
| mysub <- mysub | |
| } | |
| ## Plot ellipse | |
| plotellipse <- function (center=c(1,1), radius=c(1,2), rotate=1, segments=360, xlab="", ylab="", ...) { | |
| angles <- (0:segments) * 2 * pi/segments | |
| rotate <- rotate*pi/180 | |
| ellipse <- cbind(radius[1] * cos(angles), radius[2] * sin(angles)) | |
| ellipse <- cbind( ellipse[,1]*cos(rotate) + ellipse[,2]*sin(rotate), ellipse[,2]*cos(rotate) - ellipse[,1]*sin(rotate) ) | |
| ellipse <- cbind(center[1]+ellipse[,1], center[2]+ellipse[,2]) | |
| plot(ellipse, type = "l", xlim = c(0, 10), ylim = c(0, 10), xlab = "", ylab = "", ...) | |
| } | |
| ## Plot ellipse as 5-way venn diagram | |
| ellipseVenn <- function(...) { | |
| split.screen(c(1,1)) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(4.83,6.2), radius=c(1.43,4.11), rotate=0, segments=360, xlab="", ylab="", col=lines[1], axes=FALSE, main=mymain, sub=mysub, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(6.25,5.4), radius=c(1.7,3.6), rotate=66, segments=360, xlab="", ylab="", col=lines[2], axes=FALSE, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(6.1,3.5), radius=c(1.55,3.9), rotate=150, segments=360, xlab="", ylab="", col=lines[3], axes=FALSE, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(4.48,3.15), radius=c(1.55,3.92), rotate=210, segments=360, xlab="", ylab="", col=lines[4], axes=FALSE, lwd=mylwd, ...) | |
| screen(1, new=FALSE) | |
| plotellipse(center=c(3.7,4.8), radius=c(1.7,3.6), rotate=293.5, segments=360, xlab="", ylab="", col=lines[5], axes=FALSE, lwd=mylwd, ...) | |
| ## Add counts | |
| for(i in seq(along=counts)) { | |
| olDF <- data.frame(x=c(4.85, 8.0, 7.1, 3.5, 2.0, 5.90, 4.4, 4.60, 3.60, 7.1, 6.5, 3.2, 5.4, 6.65, 3.40, 5.00, 6.02, 3.60, 5.20, 4.03, 4.20, 6.45, 6.8, 3.39, 6.03, 5.74, 4.15, 3.95, 5.2, 6.40, 5.1), | |
| y=c(8.30, 6.2, 1.9, 1.6, 5.4, 6.85, 6.6, 2.45, 6.40, 4.3, 6.0, 4.6, 2.1, 3.40, 3.25, 6.43, 6.38, 5.10, 2.49, 6.25, 3.08, 5.30, 4.0, 3.80, 3.20, 5.95, 5.75, 3.75, 3.0, 4.50, 4.6), | |
| counts=counts[[i]]) | |
| if(colmode==1) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol, cex=ccex, ...) } | |
| if(colmode==2) { text(olDF$x, olDF$y + yoffset[i], olDF$counts, col=ccol[[i]], cex=ccex[i], ...) } | |
| } | |
| ## Add sample labels | |
| if(length(setlabels)==1 & setlabels[1]=="default") { | |
| setlabels <- names(counts[[1]][1:5]) | |
| } else { | |
| setlabels <- setlabels | |
| } | |
| text(c(5.7, 7.9, 8.5, 4.2, 0.8), c(9.9, 7.9, 1.9, 0.0, 7.3), adj=c(0, 0.5), labels=setlabels, col=lcol, cex=lcex, ...) | |
| close.screen(all=TRUE) | |
| } | |
| ellipseVenn(...) | |
| } | |
| } | |
| ############################## | |
| ## Define Bar Plot Function ## | |
| ############################## | |
| ## Plots the counts of Venn/regular intersects generated by the overLapper function | |
| olBarplot <- function(OLlist=OLlist, mycol="default", margins=c(6, 10, 3, 2), mincount=0, mysub="default", ...) { | |
| ## Generate counts and allow lower limit | |
| counts <- sapply(OLlist[[4]], length) | |
| mylogical <- counts >= mincount | |
| counts <- counts[mylogical] | |
| ## Color bars by default by complexity levels | |
| if(mycol=="default") { | |
| mycol <- OLlist$Complexity_Levels | |
| mycol <- mycol[mylogical] | |
| } else { | |
| mycol <- mycol | |
| } | |
| ## Define subtitle | |
| if(mysub=="default") { | |
| mysub <- paste("Min Count:", mincount) | |
| } else { | |
| mysub <- mysub | |
| } | |
| ## Generate bar plot with defined margins | |
| par(mar=margins) # Define margins to allow long labels | |
| barplot(counts, col=mycol, sub=mysub, ...) | |
| par(mar=c(5, 4, 4, 2) + 0.1) # Set margins back to default | |
| } |
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