Local Clustergrammer API¶
local new module
-
class
clustergrammer_py.
Network
¶ Bases:
object
version 1.2.1 Modifying API
Networks have two states:
- the data state, where they are stored as a matrix and nodes
2) the viz state where they are stored as viz.links, viz.row_nodes, and viz.col_nodes.
The goal is to start in a data-state and produce a viz-state of the network that will be used as input to clustergram.js.
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Iframe_web_app
(filename=None, width=1000, height=800)¶
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dat_to_df
()¶ convert from clusergrammers dat format to pandas dataframe
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df_to_dat
(df)¶ Convert from pandas dataframe to clustergrammers dat format (will be deprecated)
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enrichr
(req_type, gene_list=None, lib=None, list_id=None, max_terms=None)¶ under development, get enrichment results from Enrichr and add them to clustergram
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export_df
()¶ export dataframe from network
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export_net_json
(net_type='viz', indent='no-indent')¶ export dat or viz json
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filter_N_top
(inst_rc, N_top, rank_type='sum')¶ Filter a network’s rows or cols based on sum/variance, and only keep the top N
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filter_sum
(inst_rc, threshold, take_abs=True)¶ Filter a network’s rows or columns based on the sum across rows or columns Works on the network object
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filter_threshold
(inst_rc, threshold, num_occur=1)¶ Filter a network’s rows or cols based on num_occur values being above a threshold (in absolute value)
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load_data_file_to_net
(filename)¶ load my .dat format (saved as json) for a network to a netowrk
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load_df
(df)¶ Upload pandas datafraeme
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load_file
(filename)¶ load file to network, currently supporting only tsv
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static
load_gmt
(filename)¶
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static
load_json_to_dict
(filename)¶
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load_stdin
()¶ load stdin tsv formatted string
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load_tsv_to_net
(file_buffer, filename=None)¶ This will load a tsv matrix file buffer, this is exposed so that it will be possible to load data without having to read from a file.
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load_vect_post_to_net
(vect_post)¶ load vector format to network
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make_clust
(dist_type='cosine', run_clustering=True, dendro=True, views=['N_row_sum', 'N_row_var'], linkage_type='average', sim_mat=False, filter_sim=0.1, calc_cat_pval=False, run_enrichr=None)¶ The main function run by the user to make their clustergram. views is later referred to as requested_views.
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normalize
(df=None, norm_type='zscore', axis='row', keep_orig=False)¶ under development, normalize the network rows/cols using zscore
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produce_view
(requested_view=None)¶ under development, will produce a single view on demand from .dat data
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reset
()¶ function for user to reset network
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static
save_dict_to_json
(inst_dict, filename, indent='no-indent')¶
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swap_nan_for_zero
()¶
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widget
()¶ export viz json, for use with clustergrammer_widget
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write_json_to_file
(net_type, filename, indent='no-indent')¶
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write_matrix_to_tsv
(filename=None, df=None)¶