I have data which looks like this:
chr01 chr02 chr03 chr04 chr05 chr06 chr07 chr08 chr09
T10 2 5 3 5 4 1 9 2 3
T11 0 2 1 5 2 1 3 5 4
T65 0 5 1 3 4 1 5 3 1
Some of the columns columns have 0's. I want to visualize the number of zeros in each column (may be as a percentage content of 0 for each column). I am an R user, first I thought of using pie chart but I was wondering is there any sophisticated way of representing it !?
Even I tried heatmap. Any other way to represent this?? (bottom line is I want to represent percentage of 0's per column wise)
You could also use ggplot2. It gives you more control, although I am not sure if that's the eye-candy you're looking for. I am not sure if you are asking for a completely different type of visualisation or if you're looking for plotting a bar-plot (which is appropriate here as
@Didzis showed) with more control. For the 2nd case,
ggplot2 might be useful:
require(ggplot2) df <- structure(list(chr01 = c(2L, 0L, 0L), chr02 = c(5L, 0L, 5L), chr03 = c(3L, 1L, 0L), chr04 = c(0L, 5L, 0L), chr05 = c(0L, 2L, 4L), chr06 = c(0L, 0L, 0L), chr07 = c(9L, 3L, 0L), chr08 = c(2L, 0L, 3L), chr09 = c(3L, 4L, 1L)), .Names = c("chr01", "chr02", "chr03", "chr04", "chr05", "chr06", "chr07", "chr08", "chr09" ), class = "data.frame", row.names = c("T10", "T11", "T65")) gg.df <- data.frame(chr.id = names(df)) gg.df$cnt <- sapply(df, function(x) sum(x==0)/length(x) * 100) qplot(factor(chr.id), weight=cnt, data=gg.df, geom="bar", fill=factor(chr.id))
This gives you: .
Of course you can change every element of this plot (check out the link at the beginning of this post).
Another way is to use
dotplot - where you only represent your values by a single dot. I would use package lattice to do this instead of ggplot2, but I added both solutions below just in case:
#load df data from @Arun answer, and then... library(reshape2)#for melt function dd <- apply(df,2,function(x) mean(x==0)*100) d1 <- melt(dd)#gets data to long format d <- data.frame(variable=rownames(d1), d1) #lattice dotplot library(lattice) dotplot(reorder(variable, value) ~ value, d, col=1, aspect=1, xlab="percentage", ylab="")
#ggplot2 dotplot library(ggplot2) ggplot(d, aes(x = value, y = reorder(variable, value))) + labs(x = "percentage", y = "") + geom_point() + theme_bw()
Simple way to represent results is to make bar plot. Assuming that your data frame is named
#Calculate percentage of 0 for each column pr.0<-apply(df,2,function(x) mean(x==0)*100) #Plot results barplot(pr.0,ylab="Percentage")