cocoatree.visualization.update_tree_ete3_and_return_style

cocoatree.visualization.update_tree_ete3_and_return_style(tree_ete3, df_annot, sector_id, sector_seq, meta_data, fig_title='', t_sector_seq=True, t_sector_heatmap=True, colormap='inferno')

Update ete3 tree with sector info and attributes and return tree_style for further visualization.

Arguments

tree_ete3ete3’s tree object,

as imported by io.load_tree_ete3()

annot_file : pandas dataframe of the annotation file

sector_idlist of sector identifiers, as imported by io.load_msa()

the ids must match with the tree’s leaves id

sector_seqcorresponding list of sector sequences to display,

as imported by io.load_msa()

meta_datatuple of annotations to display

(from annotation file’s header)

fig_title : figure title (str)

t_sector_seqboolean,

whether to show the sequences of the sector

t_sector_heatmapboolean,

whether to add a heatmap of the identity matrix between sector sequences

Returns

tree_style : TreeStyle class from ete3

Examples using cocoatree.visualization.update_tree_ete3_and_return_style

Plot sector together with (phylogenetic) tree and metadata

Plot sector together with (phylogenetic) tree and metadata