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Plotting loci

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nyoungb2 edited this page Sep 19, 2013 · 3 revisions

Preamble

Multiple elements can be used to create a loci plot from CLdb. These include:

  • A 'dna_segs' table (required). This includes start-stop info for all CRISRP and gene features.

  • An 'xlims' table (required). This provides the start-stop of the loci to plot.

  • A tree showing loci relatedness. This orders the loci by the tree.

  • A 'comparisons' table. This shows comparisons (e.g. BLASTp) between spacers or genes from adjacent loci in the plot.

The plotting script names have the table name involved first (e.g CLdb_dna_segs_make.pl), so hopefully they are easier to find by tab-completion

Making a dna_segs table

Just selecting Subtype I-A in this example:

$ CLdb_dna_segs_make.pl -d CLdb.sqlite -sub I-A > dna_segs_I-A.txt

Also get gene cluster information from an ITEP database:

$ CLdb_dna_segs_make.pl -d CLdb.sqlite -sub I-A -I DATABASE.sqlite all_I_2.0_c_0.4_m_maxbit > dna_segs_I-A.txt

Just completely intact loci (no 'broken')

$ CLdb_dna_segs_make.pl -da CLdb.sqlite -sub I-A -q "AND loci.operon_status != 'broken'" > dna_segs_I-A.txt

Making an xlims table

Just subtype I-A in this example:

$ CLdb_xlims_make.pl -da CLdb.sqlite -sub I-A > xlims_I-A.txt

Just completely intact loci (no 'broken')

$ CLdb_xlims.pl -da CLdb.sqlite -sub I-A -q "AND loci.operon_status != 'broken'" > xlims_I-A.txt

Ordering the dna_segs table by a tree

Needed if a tree is added to the plot. The tree is pruned to just the taxa in the dna_segs table. Leaves will be added if any taxa have multiple loci in the dna_segs table.

$ CLdb_dna_segs_orderByTree.pl -t tree.nwk < dna_segs.txt > dna_segs_order.txt

Ordering the xlims table by a tree

Needed if a tree is added to the plot. The same tree editting will be done as with a dna_segs table, but an editted tree will not be written.

$ CLdb_dna_segs_orderByTree.pl -t tree.nwk < xlims.txt > xlims_order.txt

Making a comparisons table

Use an tree-ordered dna_segs table if plotting with a tree

$ CLdb_comparison_make.pl -da CLdb.sqlite < dna_segs_order.txt > comparisons.txt

Formatting colors of genes, spacers, and direct repeats

This will make the feature colors more discernable and remove any coloring that is not needed to descriminate related features in different loci (i.e. coloring is not needed if a related feature is only found in adjacent loci and comparisons are connecting them all).

$ CLdb_dna_segs_formatColor.pl -c comparisons.txt < dna_segs_order.txt > dna_segs_order_col.txt

Plotting with R functions

A set of functions can be used to pull in and do some final edits on all of the plot elements (tables & tree). These functions (along with an example at the end of the script) are found in:

CLdb_loci_plot_func.r

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