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Wrh.dev#90

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weshorton wants to merge 25 commits intobioconductorFertigLab/dominoSignal:bioconductorfrom wrh.devFertigLab/dominoSignal:wrh.devCopy head branch name to clipboard

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Commits on Feb 22, 2024

• Long commit, forgot to commit while working.

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Commits on Feb 23, 2024

• Update man for circos plot to include title

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• Update incoming_signaling_heatmap man to have the new display arguments (don't work rn b/c that bit is commented out)

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• Forgot to add the descriptions to incoming_signaling_heatmap

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• Update signaling_network man to have offset_sides option

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• Fix display_top/display_method mixup between signaling_heatmap and incoming_signaling_heatmap man sections.

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Commits on Feb 26, 2024

• Add 'cr_signaling_matrices' and 'rec_signaling' slots to domino class definition

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• New function make_rl_reading that takes the rl_reading construction out of and turns it into a function. Replace loop in create_domino with new function

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• Revert "New function make_rl_reading that takes the rl_reading construction out of and turns it into a function. Replace loop in create_domino with new function"

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• Add new function that is reverse of circos_ligand_receptor. To do: combine these two functions

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• Update dom_linkages access function to recognize lig_rec

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• New function that takes a built domino object and calculates receptor expression by cluster and makes a ligand-receptor map

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• Updated man file for linkages script

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• Update feature heatmap to subset for specific clusters

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• Update namespace with new functions

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Commits on Feb 28, 2024

• Part 1 of large update to Sushma's outgoing_network code.

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• Part 2 of large update to Sushma's outgoing_network code.

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• Add lig_rec to dom@linkages in create_domino

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• Combined both circos plot versions into one generalized plot. Remove the ligand one, keep the original receptor one but deprecated

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• Add note to build_domino about possibly getting list of expressed ligands

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• Add circos_ligand_receptor_general to NAMESPACE and remove circos_receptor_ligand

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• Add verbose option to outgoign_network to update which cluster is being run (since it takes a while)

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Commits on Feb 29, 2024

• Add help markdown to circos_ligand_receptor_general. Also add multi_plot option

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Commits on Mar 1, 2024

• Update gene_network function. Fixed the L_ substitution because it gets 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…

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Commits on Jul 9, 2024

• Changed stop()'s to warnings()'s for expression check so I can run circos_ligand_receptor_general in a loop without it breaking.Added a which_v option to indicate whether receptor or ligand should …

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