VERSION 1.5.4
-------------

  o adjust run-time messages into 3 consistent classes: Info (on
    progress), Note and Warning.

  o include paths.hsa data, the full list of human pathway ID/names
    from KEGG, as to help user specify target pathways when calling
    pathview.

  o updated korg to included over 80 newly added species, such as
    sheep, apple, mandarin orange etc. Pathview can work with 3050
    species now.

  o adjust the definitions of 7 arguments for pathview function:
    discrete, limit,bins, both.dirs, trans.fun, low, mid, high. These
    used to be a list of two logical elements with "gene" and "cpd" as
    the names. They can be vectors of two or one element(s) now. This
    makes pathview easier to use now.

  o Vigette has been reformatted: add a Citation section, and some
    example on reading user data into R, fix a few typos.


VERSION 1.4.2
-------------

  o fixed bug in render.kegg.node function, which generates black
    lines in some nodes of multiple sample view.

VERSION 1.3.6
-------------

  o ajusted node x coordinate by +0.5 to better fit the color blocks
    in 2 layer native kegg views.

VERSION 1.3.4
-------------

  o updated bods to included an extra column of id.type, the default
    gene ID type.


VERSION 1.2.4
-------------

  o updated korg to included over 600 newly added species. Pathview
    can work with 2970 species now.

  o Make returned values from pathview, keggview.native and
    keggview.graph functions invisible.

VERSION 1.2.3
-------------

  o Fixed bug in node.map function, which produces 0 values when all
    multiple genes in a node are NA's.

VERSION 1.2.2
-------------

  o Fixed bug in mol.sum function, which generates "incorrect number of
    dimension" or NA's when sum.method="median" etc.

VERSION 1.2.1
-------------

  o Fixed bug in "missing red disease gene node labels" in diease
    pathways. To avoid interfering with node coloring, set all disease
    gene labels to black instead.

VERSION 1.1.7
-------------

  o Graphviz view can automatic choose different types of legends,
    either on nodes, edges or both depending on the specific pathways.

  o Vigette has been reformatted: the "Quick start" section added

VERSION 1.1.6
-------------
  o Pathview can plot/integrate/compare multiple states/samples in the
    same graph. Several functions and data objects are revised:
    including pathview, keggview.native, keggview.graph,
    render.kegg.node etc. New section on multiple state data with
    working exampleshas been added.

  o Vigette has been reformatted: Data integration section splitted
    into multiple sub-sections.

VERSION 1.1.5
-------------
  o Pathview works with species where default KEGG gene ID is not
    Entrez Gene. Several functions and data objects are revised:
    including pathview, node.map, sim.mol.data, kegg.species.code,
    korg. New section on KEGG species and Gene ID usage with working
    exampleshas been added.

VERSION 1.1.3
-------------
  o Pathview paper published in Bioinformatics

VERSION 1.0.0
-------------
  o Initial release with Bioconductor

  o Main function: pathview

  o Four functional modules: 
    -Downloader: download.kegg;
    -Parser: node.info, combineKEGGnodes, reaction2edge;
    -Mapper: node.map, eg2id, id2eg, cpdkegg2name, cpdname2kegg,
    	     cpd2kegg, cpdidmap, kegg.species.code, mol.sum, 
	     sim.mol.data;
    -Viewer: keggview.native, keggview.graph, node.color, 
    	     col.key, wordwrap, strfit