Changes in version 0.2.5                        

  - renamed package to lowercase goatea
  - fixed dplyr %>% pipelines with .data$undefined_var_names
  - fixed subgraphing/filtering by highlighting clusters/features
      - noted that highlighted but isolated (disconnected) nodes are not
        graphed
      - noted that clustering of the selected proteins is kept, unless
        if the proteins selected all belong to the same cluster
  - fixed object g not found error by getting it from reactive value
  - added save to R base folder and load loaded_taxid_genesets.Rdata
    functionality
  - added showNotification for ppi subgraph and subheatmaps
  - fixed alignment of signif and signif_overlap in gene*geneset heatmap
  - if GO_BP in names, default for 'Show enrichment source'
  - transforming toupper(genelist$symbol) when mapping in order to
    format mapIds ALIAS
      - warning on %mapping not converted to ENTREZIDs
  - noted to download org.Xx.eg.db manually!
  - fixed reloading data by resetting earlier loaded data, requiring to
    load all wanted data in one upload
  - set contentType to NULL on downloadHandlers to use global format
    parameter for tables to auto use .csv or .xlsx
  - kept only explicit ::fromList() calls instead of importFrom UpSetR
    or upsetjs to remove message for BiocCheck
  - added showNotifications when gene selection buttons clicked

                        Changes in version 0.2.0                        

  - added priority of selected genes to gene*set heatmap
  - fixed setting names to updateSelectInputs and updating names in
    gene_overview
  - set all :: and/or importFrom for R CMD check/BiocChecks
  - for gene*effectsize heatmap: fixed setting as many genes in
    annotation as in matrix

                       Changes in version 0.1.19                        

  - visnetwork ppigraphs hover tooltip background and labels colored via
    JavaScript such that it is readable
    (www/visnetwork_hover_tooltip_style.js)
  - genes*genesets heatmap: showing top genes based on ordering by
    highest ncount in terms and then highest effectsize
  - fixed interactive overlap: upsetjs::chartTheme()
  - added max gene filters to gene*geneset heatmap
  - ppi
      - fixed hover node labels with all info: added toupper() to match
        gene and protein symbols
      - fixed coloring by L2FC: added mutate(toupper()) to match gene
        and protein symbols
      - enabled entering gene/cluster to highlight or center on
      - using set_base_folder() for PPI STRINGdb downloads
      - added functionality to subgraph/filter/delete highlighted
        nodes/edges by numeric feature
  - added modal dialogues per tab
  - set_significant_N_genes: changed code order to not display warning
    when keeping max N genes

                       Changes in version 0.1.18                        

  - ppi subgraph: keep original graph clustering
  - added download button for vanilla EnhancedVolcano plot
  - Set and calculate gene_overview when setting significant genes
      - needed for ppi metadata coloring
      - moved download gene overview metadata button to 'load data' tab
        below set names
  - added interactive gene*L2FC heatmap figure for all loaded samples
    and user selected genes

                       Changes in version 0.1.17                        

  - set term n=50 and gene n=100 defaults for heatmap
  - kevinblighe/EnhancedVolcano answered issues 77/114 and
    Biostars 421750 by making minimal reproducible example of shiny +
    EnhancedVolcano + plotly for other users
  - added interactive EnhancedVolcano plot via ploty::ggplotly()

                       Changes in version 0.1.16                        

  - added interactive UpSet plot (removed Venn completely)
  - added overlap gene selection

                       Changes in version 0.1.15                        

  - started changelog
  - added to load from GMT file: goat::load_genesets_gmtfile(), label =
    "GMT")
      - checked that genesets cannot be loaded without setting 'source'
        column, for downstream processing
  - fixed run_geneset_enrichment to actually use the given parameters
  - added set_significant_N_genes() function

Future steps

  - sort heatmap by zscore (up/down regulation)
  - genefsi_icheatmap_action functionalize for
    selecting/removing/resetting genes (selection)
  - plot: similarity_heatmap(genesets/termsets) (see
    R/testing/_plot_similarity_heatmap.R)
  - volcano user label axes
  - interactive termtree
  - interactive splitdot
  - selected genes tab
  - selected terms tab (if used for plotting)
  - select genes by frequency of them popping up in terms
  - add genes to selection via input file (& custom genes selection
    tab?)
  - ppigraph: add terms as different node shape, edges to those could be
    dashes to differentiate
  - network graph
      - terms overlap by ngenes graph (connection shows overlap size,
        node size = ngenes)
          - may be able to add genes to this graph?
  - make menu_tab for colourpicker::colourInput to have user defined
    colors for plots
  - heatmap: significant genes, saturated (alpha) hue, otherwise less
    saturated
  - check heatmap y axis label lengths (going out of plot ?)