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Run eog on a plot for a clade

Source: R/eog.R
eog.Rd

Prepare a shell command to run the Eye of Gnome image viewer on a subset of alignment pairwise plots comparing genomes from the same clade.

Usage

eog(tree, node, target = NULL)

Arguments

tree

A tree created with the makeTidyTree() function.

node

The ID number of the node to base the subtree, or a FocalClade object.

target

A pattern to restrict the files to share the same target genome.

See also

Other Focal clade functions: focalClade(), recordAncestor(), recordClades(), subTree(), visualizeTree()

Author

Charles Plessy

Examples

eog(Halo_Tree, 10)
#> [1] "eog results_{Halobacterium_litoreum,Halobacterium_noricense,Halobacterium_salinarum}/alignment/*___{Halobacterium_litoreum,Halobacterium_noricense,Halobacterium_salinarum}.o2o_plt.png"
eog(Halo_Tree, 10, target = "nori")
#> [1] "eog results_Halobacterium_noricense/alignment/*___{Halobacterium_litoreum,Halobacterium_noricense,Halobacterium_salinarum}.o2o_plt.png"
eog(Halo_Tree, Halo_FocalClades$Haloferax)
#> [1] "eog results_{Haloferax_mediterranei,Haloferax_volcanii}/alignment/*___{Haloferax_mediterranei,Haloferax_volcanii}.o2o_plt.png"