ceqlogo [ -i <motif file> -m <id> | -i<id> <motif file> ]+ [options]
Load all motifs within a MEME motif file and write to logo.eps in EPS format:
ceqlogo -i meme.motifs -o logo.eps -f EPS
Load second motif from each of two files and shift the first one:
ceqlogo -i2 meme1.motifs -s 3 -i2 meme2.motifs -o logo.eps -f EPS
The ceqlogo program generates one or multiple, aligned logos in EPS
or PNG format, based on a set of frequency matrices provided in the
MEME file format.
The code of ceqlogo is based on the Perl code of
weblogo but is written in C
and supports PNG output. Note that the program strives to use command
line options similar to those of weblogo.
The letter stacks are calculated by the following equations found in Schneider and Stephens paper "Sequence Logos: A New Way to Display Consensus Sequences" and adapted from the weblogo documentation. The height of a letter is calculated as:
height(b,l) = f(b,l) * R(l)
where f(b,l) is the frequency of base or amino acid
b at position l. The stack height
R(l) is the amount of information present at position
l and can be quantified as follows:
R(l) for amino acids = log(20) - (H(l) + e(n))
R(l) for nucleic acids = 2 - (H(l) + e(n))
where log is taken base 2,
H(l) is the uncertainty at position l, and
e(n) is the error correction factor for small sample sizes
n. H(l) is computed as follows:
H(l) = - (Sum f(b,l) * log[ f(b,l) ])
where again, log is taken base 2.
f(b,l) is the frequency of base b at position
l. The sum is taken over all amino acids or bases.
The error correction factor e(n) is approximated by:
e(n) = (s-1) / (2 * ln 2 * n)
A file containing one or more motifs in MEME format.
If no output file is specified ceqlogo writes to standard output.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| Options with arguments | |||
| -i | motif file | Load all motifs within the motif file. | |
| -m | id or num | Load the numth motif or the motif whose ID is id within the motif file specified by the previous -i option. | |
| -ix | motif file | Load the xth motif or the motif whose ID is x within the motif file. | |
| -r | Reverse-complement the logo for the previous -i or -m option. | ||
| -l | Load motifs by IDs, preferentially. | Load motifs in input order, preferentially. | |
| -s | shift | Offset the previously loaded motif by shift. | -b | bar bits | Number of bits in bar (real # > 0). | DNA motifs have a default height of 2 bits and protein motifs have a default height of 4.3 bits. |
| -c | tic bits | Number of bits between tic marks. | |
| -e | error bar fraction | Fraction of error bar to show (real # > 0). | |
| -f | EPS|PNG | Set the format of the output. | The output is created in EPS. |
| -F | Create a frequency logo with stack height 1. | Height of stack is information content of motif column. | |
| -h | logo height | Height of output logo in cm (real # > 0). | |
| -o | image file | Create an image called image file and send the output to it. | Send the output to standard out. |
| -n | sample number | Set the sample count of the previously loaded motif to sample number. This value is used to calculate error bars. | Use the sample count embeded in the motif file. |
| -t | title label | Set the title of the image to title label. | |
| -w | logo width | Width of output logo in cm (real # > 0) | |
| -x | x-axis label | Label for x-axis. | |
| -y | y-axis label | Label for y-axis. | |
| -p | pseudocount | Pseudocount for motifs. | A pseudocount value of 1 is used. |
| -d | fineprint | Print fineprint in small font at bottom of logo. | "Ceqlogo |
| --test | verbosity level | Runs a self test, ignoring all other options. The verbosity level [0..3] is optional. | |
| Toggles | |||
| -S | Turn off small sample correction. | Small sample correction is used. | |
| -B | Toggle bar ends. | ||
| -E | Toggle error bar. | ||
| -O | Toggle outlining of characters. | ||
| -N | Toggle numbering of x-axis. | ||
| -X | Toggle boxing of characters. | ||
| -Y | Toggle y-axis. | ||