centrimo-plots [options]
Reads 'centrimo' text output (site_counts.txt) and creates a plot with the site-probability curves for the motifs with the lowest central enrichment p-values: 'combined.png'. Creates a text file listing the central enrichment statistics for all significantly enriched motifs: 'centrimo.txt'.
Reads centrimo text output (site_counts.txt) from standard input.
CentriMo Plots outputs a text file called centrimo.txt which gives information on which motifs are most centrally enriched. If you have gnuplot installed it also creates a combined plot showing the output site probability curves for the top motifs (PNG and EPS format). If -indiv is specified then it will create individual plots for each significant motif.
| Option | Parameter | Description | Default Behaviour |
|---|---|---|---|
| Input/Output | |||
| -o | <directory> | Create the directory and write output files in it. This option is not compatible with -oc as only one output directory is allowed. | The program behaves as if -oc centrimo-plots_out
had been specified. |
| -oc | <directory> | Create the directory but if it already exists allow overwriting the contents. This option is not compatible with -o as only one output directory is allowed. | The program behaves as if -oc centrimo-plots_out had been specified. |
| Plots | |||
| -indiv | Output a site-probability plot for each motif. | Only combined plot is created. | |
| -max | <N> | Output site-probability curves for the <N> motifs with the lowest central enrichment p-values on a single plot. | Up to 5 plots are combined. |
| -ethresh | <e> | only output results with E-value <= <e> | A theshold of 10 is used. |
| -bin | <size> | The size of bins for smoothing plotted data. If the bin size is 1 then it displays error bars. | A bin size of 10 is used. |
| -title | <title> | Print <title> as part of plots. | No title. |
| -rescale | Put all plots on the same Y axis. | Don't rescale plots. | |
| -miny | <miny> | A minimum y scale of 0 is used. | |
| Miscellaneous | |||
| -h | Print a help message and exit. | Continue as normal. | |