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proteomaps

Scripts and data for generating proteome treemaps (AKA proteomaps)

File descriptions

  • ./data/KO_gene_hierarchy/KO_gene_hierarchy_changes.csv : Table with our own gene reannotations
  • ./data/KO_gene_hierarchy/KO_gene_hierarchy_colors.csv : Table with colors for 2nd-level categories
  • ./data/KO_gene_hierarchy/KO_gene_hierarchy_organism_mapping/[ORGANISM]_mapping.csv : contains organism-specific ID mapping from KO to the relevant genomic annotations with the following columns [Systematic name] // [Gene name] // [KO number]

Procedure for drawing a proteomap using Paver

File -> New -> Treemap -> Simple format select the Hierarchy file (proteomaps/res/[ORGANISM]_hierarchy.tms)

Data -> Load Cell Sizes -> CSV Cell Size Data select the abundance data file (proteomaps/data/proteomic_data/[ORGANISM]_[CONDITION]_cost.csv)

Colors -> Load Colors select the color scheme table (proteomaps/data/KO_gene_hierarchy/KO_gene_hierarchy_colors.csv)

File -> Save Visualization res/[ORGANISM]_[CONDITION]_cost.xml

If the organism has more than one condition, use the first condition as a template and load the cell sizes on top of that in order to have similarly placed cells.