pathview/NEWS at master · ZhaoJK/pathview · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
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