VERSION 1.31.3/1.30.3
-------------
o fix bug in mol.sum with single gene data reported by
easygsea. Similarly add drop=F to a few other lines in mol.sum and
node.map.
VERSION 1.31.2/1.30.2
-------------
o solve the check error due to the change related to KEGGEdgeSubtype
in KEGGgraph package (version 1.51.1).
VERSION 1.31.1/1.30.1
-------------
o korg now include 6833 KEGG species or 1588 new species beyond 2017.
VERSION 1.29.1/1.28.1
-------------
o developmental version now available on GitHub at:
https://github.com/datapplab/pathview
o fixed warning on "requireNamespace(pkg.name)" in geneannot.map.R
and sim.mol.data.R. Now "import" from org.Hs.eg.db, instead of
"suggest" it. Also import more functions and class from
AnnotationDbi.
o prevented potential error caused by class(exprs) == "data.frame"
or "class()==" if conditions in multiple functions. class(exprs)
now returns a vector of length 2, which caused the error.
VERSION 1.23.3/1.22.3
-------------
o fix error and warning cause by geneannot.map() function. change
if(in.type == out.type) to if(all(in.type == out.type)). change
biocLite installation to BiocManager::install. make similar changes
in sim.mol.data() function.
o update NAMESPACE file on importFrom lines on AnnotationDbi and
BiocManager.
VERSION 1.18.2
-------------
o korg now include 5245 KEGG species. To speed up pathview package
loading, an updated version of korg is now checked out from
Pathview Web server only when it is acutally used and needed.
VERSION 1.17.7
-------------
o updated combineKEGGnodes.R, i.e. changed the stop error to a
warning message when a group node include different node types,
i.e. both gene and compound. This problematic KEGG node definition
does exist in pathway 04136 Autophagy - other, and caused error
when calling pathview with kegg.native = F.
o fixed bug in mol.sum introduced at 1.15.1, i.e. indexing using
which(eff.idx). This problem only affect direct call of mol.sum
with sum.method other than "sum" and "mean".
VERSION 1.17.1
-------------
o major expansion in korg, which now include both KEGG and NCBI
taxonomy IDs, two more gene ID types, i.e. NCBI protein and uniprot
IDs. In addition, Entrez or NCBI Gene IDs are discontinued for most
prokaryotes.
o korg now include 4800 KEGG species, in the meantime, an updated
version of korg is now checked out from Pathview Web server each
time pathview package is loaded.
VERSION 1.15.1
-------------
o fixed bug in node.map on single row/mapped data, and in mapped row
numbers.
VERSION 1.10.2
-------------
o fixed problem that no node mapped when one gene/protein ID maps to
multiple Entrez Gene ID (like Enzyme IDs): id2eg call with unique.map=F.
VERSION 1.10.1
-------------
o fix bug in reaction2edge function, which throw error for a few
metabolic pathways with no multi-node reaction group (examples
including 00072, 00100).
VERSION 1.9.3
-------------
o pathview can accept a vector of multiple pathway ids, and
map/render the user data onto all these pathways in one call.
o one extra column "all.mapped" was added to pathview output
data.frames as to show all the gene/compound IDs mapped to each
node.
o add geneannot.map as a generic function for gene ID or annotation
mapping.
o sim.mol.data now generate data with all major gene ID types for
all 19 species in bods, not just human.
o download.kegg now let the user to choose from xml, png or both
file types to download for each input pathway. In the meantime, it
uses the KEGG REST API instead of the classical KEGG download
links. All potential pathways including the general pathways can be
downloaded this way.
o solve the redundant import from graph package.
o import specific instead of all functions from XML package.
VERSION 1.9.1
-------------
o solve the install error due to the recent change in KEGGgraph
package.
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