inst/report_binned_seqs.md

In philliplab/MotifBinner: Bin reads by Motif

The unprocessed bins produced

Sys.time()

## [1] "2015-03-19 13:25:20 SAST"

The number of bins

print(length(bin_seqs))

## [1] 998

The sizes of the bins

bin_sizes <- unlist(lapply(bin_seqs, length))
hist(bin_sizes)

kable(data.frame(bin_size = as.numeric(names(table(bin_sizes))),
                 num_bins = as.numeric(table(bin_sizes))))

| bin_size| num_bins| |--------:|--------:| | 1| 482| | 2| 76| | 3| 35| | 4| 32| | 5| 24| | 6| 20| | 7| 9| | 8| 13| | 9| 9| | 10| 17| | 11| 15| | 12| 10| | 13| 8| | 14| 6| | 15| 6| | 16| 10| | 17| 9| | 18| 8| | 19| 11| | 20| 9| | 21| 5| | 22| 8| | 23| 5| | 24| 5| | 25| 4| | 26| 6| | 27| 6| | 28| 4| | 29| 8| | 30| 8| | 31| 5| | 32| 4| | 33| 4| | 34| 4| | 35| 5| | 36| 3| | 37| 7| | 38| 3| | 39| 5| | 40| 4| | 41| 3| | 43| 3| | 44| 5| | 45| 2| | 46| 5| | 47| 1| | 49| 4| | 51| 1| | 52| 1| | 53| 1| | 54| 1| | 55| 6| | 56| 1| | 57| 3| | 58| 1| | 59| 1| | 60| 3| | 61| 1| | 62| 2| | 63| 1| | 65| 5| | 66| 3| | 67| 3| | 68| 3| | 70| 1| | 73| 4| | 75| 1| | 76| 1| | 77| 1| | 80| 1| | 81| 2| | 82| 1| | 85| 1| | 86| 2| | 87| 1| | 94| 2| | 96| 1| | 97| 2| | 100| 1| | 101| 1| | 103| 1| | 113| 1| | 119| 1|

scatter and log log plot of the bin sizes

loglog <- data.frame(bin_size = as.numeric(names(table(bin_sizes))),
                     num_bins = as.numeric(table(bin_sizes)))
plot(num_bins ~ bin_size, data = loglog)

plot(log10(num_bins) ~ log10(bin_size), data = loglog)

Categories and count frequencies

cats <- hist(bin_sizes, breaks = c(0,1,2,3,4,10,20,400,1000000), plot=FALSE)
counts <- cats$counts
names(counts) <- paste('(', cats$breaks[1:(length(cats$breaks)-1)], 
                  '-', cats$breaks[2:(length(cats$breaks))], ']',
                  sep='')
names(counts)[length(counts)] <- paste(cats$breaks[length(cats$breaks)-1], '+',
                                       sep = '')
barplot(counts, main = 'Histogram of Bin Sizes')

kable(data.frame(category = names(counts),
                 count = counts,
                 row.names = 1:length(counts)))

|category | count| |:--------|-----:| |(0-1] | 482| |(1-2] | 76| |(2-3] | 35| |(3-4] | 32| |(4-10] | 92| |(10-20] | 92| |(20-400] | 189| |400+ | 0|

philliplab/MotifBinner documentation built on Sept. 2, 2020, 11:41 a.m.