Wrh.dev #25
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Wrh.dev #25
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Definition of the linkage summary class added to facilitate comparisons of linkages established in domino objects across sample covariates.
updating readme with archived versions of domino from publication.
also includes a bug fix where lists of linkage counts were being saved into the resulting data frame instead of a numeric vector.
Changed base from master to alt_gene_conversions_&_class_checks to integrate with compare_linkages changes intended for v0.2.2
Changed base from master to alt_gene_conversions_&_class_checks to integrate with compare_linkages changes intended for v0.2.2
Changed base from master to alt_gene_conversions_&_class_checks to integrate with compare_linkages changes intended for v0.2.2
Removed deleted function get_regulon_info
This reverts commit c34d66f.
(1) Start an attempt to subset the ligands output in incoming signaling heatmap. Having trouble getting color scale for the subset. (2) Add option to signaling_network to adjust offset for labels that end up on the left and right sides of the plot (3) Also changed label distance in signaling_network - can this be an option? (4) Add circle.margin to circos plot generation in order to have space for legend and title. Can this either be supplied using ... as is, or is there a better way to not hard-code this? (5) Update circos plot to be able to make a plot using only a subset of the populations.
…ts (don't work rn b/c that bit is commented out)
…coming_signaling_heatmap man sections. Updates to feat_heatmap: (1) New 'clust' argument to provide a vector of clusters for display (instead of all clusters) (2) Add cell names to cl as names in order to sort table appropriately (3) remove because the above does the sort now (and this didn't work) (4) Updated to provide a warning if data has a cluster that isn't provided in the cols argument and then creates a randomly generated color for it
…ut of and turns it into a function. Replace loop in create_domino with new function
…uction out of and turns it into a function. Replace loop in create_domino with new function" This reverts commit 0f34cf1.
…mbine these two functions
… expression by cluster and makes a ligand-receptor map
1. Added markdown to resolve_names and resolve_complexes 2. Updated resolve_names to resolve receptors or ligands 3. get_all_reclig is a function made from first bit of original outgoing_network. Returns all ligands or all receptors in the domino object
1. add markdown to avg_exp_for_complexes 2. Extract receptor/ligand average expression loop from outgoing_network and put in own function - avg_reclig_expr 3. New function invert_rec_lig_linkages that adds dom@linkages, which is inverse of dom@linkages 4. New function invert_rec_lig_expr that adds dom@cr_signaling_matrices and dom@rec_signaling 5. Add sushma's outgoing_network function, with markdown and all these new functions included. Extend functionality to include the receptor in the receiving cluster's expression.
…the ligand one, keep the original receptor one but deprecated
…ng run (since it takes a while)
…ts messed up in the for loop. Also subset the input clusters in case they're not expressed in the object. Also added a new title option
…rcos_ligand_receptor_general in a loop without it breaking.Added a which_v option to indicate whether receptor or ligand should be used (so that you can subset the pair). Example, if plotting a receptor with 5 ligands, you can now specify which of those 5 ligands you want to include in the plot, instead of all 5.
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Testing draft pull request