I have a dataframe:
>picard
count reads
1 20681318
2 3206677
3 674351
4 319173
5 139411
6 117706
How do I plot log10(count) vs log10(reads) on a ggplot (barplot)?
I tried:
ggplot(picard) + geom_bar(aes(x=log10(count),y=log10(reads)))
But it is not accepting y=log10(reads). How do I plot my y values?
You can do something like this, but plotting the x axis, which is not continuous, with a log10 scale doesn't make sense for me :
ggplot(picard) +
geom_bar(aes(x=count,y=reads),stat="identity") +
scale_y_log10() +
scale_x_log10()
If you only want an y axis with a log10 scale, just do :
ggplot(picard) +
geom_bar(aes(x=count,y=reads),stat="identity") +
scale_y_log10()
width argument of geom_bar().
Use stat="identity":
ggplot(picard) + geom_bar(aes(x=log10(count),y=log10(reads)), stat="identity")
You will actually get a warning with your approach:
Mapping a variable to y and also using stat="bin". With stat="bin", it will attempt to set the y value to the count of cases in each group. This can result in unexpected behavior and will not be allowed in a future version of ggplot2. If you want y to represent counts of cases, use stat="bin" and don't map a variable to y. If you want y to represent values in the data, use stat="identity". See ?geom_bar for examples. (Deprecated; last used in version 0.9.2)
There's a direct way to do this, i.e. by using the geom_col() function. Just make a tiny adjustment to your code:
ggplot(picard) + geom_col(aes(x=log10(count), y=log10(reads)))
and it will give the same output as setting the stat argument to identity with geom_bar(). The thing is, geom_bar() uses count as default for stat, hence it will not take any variable for the y-axis. It will simply use the count, i.e, the number of occurrences of each value of the x-axis, for it's y-axis. I hope this answers your question.
