fixSetLabels: Fix Set labels for legibility

In jmw86069/multienrichjam: Analysis and Visualization of Multiple Gene Set Enrichments

Fix Set labels for legibility

Description

Fix Set labels for legibility

Usage

fixSetLabels(
  x,
  wrap = TRUE,
  width = 40,
  maxNchar = Inf,
  suffix = "...",
  nodeType = c("Set", "Gene", "any"),
  do_abbreviations = TRUE,
  adjustCase = TRUE,
  lowercaseAll = TRUE,
  removeGrep = "^(KEGG|PID|REACTOME|BIOCARTA|NABA|SA|SIG|ST|WP|HALLMARK)[_. ]",
  words_from = c("als", "ii", "iii", "iv", "v", "vi", "Vii", "Viii", "ix", "x", "trna",
    "rrna", "rna", "dna", "mirna", "mrna", "snrna", "snorna", "scrna", "lincrna", "Il",
    "Ecm", "Nk", "Pi3k.Akt", "Akt", "Pi3k", "tgf", "nfkb", "NK.Kappa.B",
    "Pi3kaktmtorsignaling", "Pi3kaktmtor", "PI3kakt", "aktmtor", "mtorsignaling",
    "Pi3kci", "Pi3kgamma", "Pi 3k", "Ppar(alpha|a)", "Ppar(gamma|g)", "Ppar",
    "Udp N Acetyl Glucosamine", "Mtor", "Gpcr", "Gpcrs", "Tnfa|Tnfalpha", "Tnfr1",
    "Tnfr2", "Tnfs", "Tnf", "Tnfsf", "Tnfrelated", 
     "Tgf(beta|b)", "Tgfbr",
    "TGF Beta", "Akt1", "Igf1akt", "Foxo", "Hdacs", "Hdac", "Hat", "Hats",
    "Nicotinic Acetylcholine Receptors|Acetylcholine Nicotinic Receptors", "G CSF",
    "Gm Csf", "M Csf", "IL([0-9]+)[-. _]([0-9]+)pathway", "Jak Stat([1-9]*)",
    "Mkk3 6pathway", "MAP([23]*)K([0-9]*)", "P38[ ]*MAPK", "MAPK1 3", "Erk MAPK", "Erk",
    "Erks", "Interferon([a-z]*)", "([A-Za-z0-9]+[a-qs-z])mediated", "Lncrna|Lincrna",
    "Microrna([s]*)", "125 DIHYDROXYVITAMIN D3", "Tweak", "Er", "Vegfavegfr2",
    "Vegfr1 2", 
     "Vegf", "Vegfr([1-9]*)", "Egfr", "Egfrviii", "Egfegfr",
    "Smad2 3(pathway|nuclear)", "Smad2 3", "Nf Kb", "Nfkappab", "C Jun", "C Fos", "Ap 1",
    "Apoe", "([AG])tpase", "Kras", "Uv", "Sarscov2", "Sars Cov ([12])", "Sars Cov",
    "Covid19", "Cellspecific", "([a-zA-Z0-9]+)like", "([TB]|NK) Cell"),
  words_to = c("ALS", "II", "III", "IV", "V", "VI", "VII", "VIII", "IX", "X", "tRNA",
    "rRNA", "RNA", "DNA", "miRNA", "mRNA", "snRNA", "snoRNA", "scRNA", "lincRNA", "IL",
    "ECM", "NK", "PI3K/AKT", "AKT", "PI3K", "TGF", "NFKB", "NFKB",
    "PI3K/AKT/mTOR Signaling", "PI3K/AKT/mTOR", "PI3K/AKT", "AKT/mTOR", "mTOR Signaling",
    "PI3KCI", "PI3Kgamma", "PI3K", "PPARalpha", "PPARgamma", "PPAR", "UDP-GlcNAc",
    "mTOR", "GPCR", "GPCRs", "TNFa", "TNFR1", "TNFR2", "TNFs", "TNF", "TNFSF",
    "TNF-related", "TGFbeta", "TGFbeta-Receptor", 
     "TGFbeta", "AKT1", "IGF1/AKT",
    "FOXO", "HDACs", "HDAC", "HAT", "HATs", "Nicotinic Acetylcholine Receptors", "G-CSF",
    "GM-CSF", "M-CSF", "IL-\\1/IL-\\2 Pathway", "JAK/STAT\\1", "MKK3/MKK6 Pathway",
    "MAP\\1K\\2", "p38-MAPK", "MAPK1/MAPK3", "ERK-MAPK", "ERK", "ERKs", "IFN\\1",
    "\\1-Mediated", "lncRNA", "microRNA\\1", "1,25-dihydroxyvitamin D3", "TWEAK",
    "ER", "VEGFA/VEGFR2", "VEGFR1/VEGFR2", "VEGF", "VEGFR\\1", "EGFR", "EGFRvIII",
    "EGF/EGFR", "Smad2/3 \\1", "Smad2/3", "NFKB", "NFKB", "C-jun", "C-fos", 
    
    "AP-1", "APOE", "\\1TPase", "KRAS", "UV", "SARS-CoV-2", "SARS-CoV-\\1",
    "SARS-CoV", "COVID19", "Cell-Specific", "\\1-Like", "\\1-cell"),
  add_from = NULL,
  add_to = NULL,
  abbrev_from = c("Extracellular.Matrix", "Mitochondri(um|a|al|on)", "Interferon",
    "(IL|Interleukin[ ]*)([0-9]+)", "Subsequent", "Signaling (pathway|system)", "Of The",
    "^Signaling by ", " Pathway[s]*$", "Expression", "The Role "),
  abbrev_to = c("ECM", "Mito", "IFN", "IL-\\2", "", "Signaling", "Of", "", "", "Expr.",
    "Role "),
  ...
)

Arguments

x	any of the following objects: character vector igraph object. The V(g)$name attribute is used as the input, and the resulting label is then stored as V(g)$label.
wrap	logical indicating whether to apply word wrap, based upon the supplied width argument.
width	integer value used when wrap=TRUE, it is sent to base::strwrap().
maxNchar	numeric value or Inf to limit the maximum characters allowed for each string. This option is preferred when wrap=TRUE is not feasible, for example heatmap labels. When NULL or Inf no limit is applied. See base::nchar().
suffix	character value, default "...", used when maxNchar is below Inf. When a string is shortened to maxNchar, the suffix helps indicate that there was additional text.
nodeType	character string ussed when x is igraph, to limit changes to nodes by attribute values in "nodeType". Use "any" or NULL to affect all nodes.
do_abbreviations	logical, default TRUE, whether to apply ⁠abbrev_from,abbrev_to⁠. These patterns are intended specifically to help shorten a long phrase, possibly removing words, or using common abbreviations.
adjustCase	logical, default TRUE, indicating whether to adjust the uppercase and lowercase lettering by calling jamba::ucfirst(). The default sets all characters to lowercase, then applies uppercase to the first letter of each word.
lowercaseAll	logical used only when adjustCase=TRUE, passed to jamba::ucfirst()
removeGrep	character regular expression pattern used to remove patterns from the resulting label. The default removes common canonical pathway source prefix terms use in MSigDB data, for example KEGG, BIOCARTA, PID, etc. Use "" or NULL to skip this step. Multiple values can be defined, they are applied in order.
words_from, words_to	character vectors of pattern, replacement, respectively. The pattern is matched in case-insensitive manner, with case-sensitive replacements where applicable. It uses perl-based regular expression matching with base::gsub(), so that the expression ⁠\\b⁠ can be used to enforce a word boundary, either via delimiter, whitespace, or the end of the string.
add_from, add_to	character vectors used in addition to words_from,words_to. These values are applied after words_from,words_to, so that user-defined replacements have priority.
abbrev_from, abbrev_to	character vectors used when do_abbreviations=TRUE. These defaults are "opinionated", they are intended to shorten common phrases which do not seem critical to understanding the meaning of most biological pathways. Some abbreviations are used for relatively common phrases and terms, for which the abbreviation seems to be unambiguous and fairly widely recognized. Examples: "Extracellular Matrix" becomes "ECM" "Mitochondrial" becomes "Mito" " Pathway" at the end of a phrase is removed, as it is not required to understand the rest of the label. "Signaling by " at the start of a phrase is removed, as it also is not typically necessary to understand the label.
...	additional arguments are passed to jamba::ucfirst(x, ...), for example firstWordOnly=TRUE will capitalize only the first word.

Details

This function is a convenient wrapper for several steps that edit gene set and pathways labels to be slightly more legible. It operates on either a character vector, or an igraph object.

• To use custom from,to replacements, along with the default replacements, supply the custom replacements with arguments add_from,add_to.

• To use custom from,to replacements, without applying the defaults, supply the custom replacements with arguments words_from,words_to.

Value

vector or igraph object, to match the input x.

See Also

Other jam igraph functions: cnet2df(), cnet2im(), cnetplotJam(), cnetplot_internalJam(), color_edges_by_nodegroups(), color_edges_by_nodes_deprecated(), color_edges_by_nodes(), color_nodes_by_nodegroups(), communities2nodegroups(), drawEllipse(), edge_bundle_bipartite(), edge_bundle_nodegroups(), enrichMapJam(), flip_edges(), get_bipartite_nodeset(), igraph2pieGraph(), jam_igraph(), jam_plot_igraph(), label_communities(), layout_with_qfrf(), layout_with_qfr(), mem2emap(), memIM2cnet(), mem_multienrichplot(), nodegroups2communities(), rectifyPiegraph(), relayout_with_qfr(), removeIgraphBlanks(), removeIgraphSinglets(), reorderIgraphNodes(), rotate_igraph_layout(), spread_igraph_labels(), subgraph_jam(), subsetCnetIgraph(), subset_igraph_components(), sync_igraph_communities(), with_qfr()

Examples

x <- c("KEGG_INSULIN_SIGNALING_PATHWAY",
   "KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY",
   "KEGG_NEUROTROPHIN_SIGNALING_PATHWAY");
fixSetLabels(x);
fixSetLabels(x, do_abbreviations=FALSE);

jamba::nullPlot();
jamba::drawLabels(txt=x,
   preset=c("top", "center", "bottom"));

jmw86069/multienrichjam documentation built on Nov. 3, 2024, 10:29 p.m.