These functions report the annotation status of the vertices of a given network, modify or remove certain annotations.
getAttrStatus(graph, pattern = "^miriam.")
getAttrNames(graph, pattern = "")
getAttribute(graph, attr.name)
setAttribute(graph, attr.name, attr.value)
rmAttribute(graph, attr.name)An annotated igraph object.
A regex experssion representing attribute name pattern.
The attribute name
A list of attribute values. This must be the same size as the number of vertices.
For getAttrStatus, a dataframe summarizing the number of vertices with no (missing), one (single)
or more than one (complex) attribute value. The coverage
For getAttrNames, a character vector of attribute names matching the pattern.
For getAttribute, a list of vertex annotation values for the query attribute.
For setAttribute, a graph with the new attribute set.
For rmAttrNames, a new igraph object with the attibute removed.
NetPathMiner stores all its vertex annotation attributes in a list, and stores them collectively as
a single attr. This is not to interfer with graph_attr_names from igraph package.
All functions here target NetPathMiner annotations only.
Other Attribute handling methods:
stdAttrNames()
data(ex_kgml_sig) # Ras and chemokine signaling pathways in human
# Get status of attribute "pathway" only
getAttrStatus(ex_kgml_sig, "^pathway$")
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...
#> missing single complex coverage.pct
#> pathway 0 90 18 100
# Get status of all attributes starting with "pathway" and "miriam" keywords
getAttrStatus(ex_kgml_sig, "(^miriam)|(^pathway)")
#> missing single complex coverage.pct
#> miriam.kegg.genes 7 49 52 94
#> miriam.ncbigene 7 49 52 94
#> miriam.kegg.pathway 0 90 18 100
#> pathway 0 90 18 100
#> miriam.kegg.compound 101 7 0 6
# Get all attribute names containing "miriam"
getAttrNames(ex_kgml_sig, "miriam")
#> [1] "miriam.kegg.genes" "miriam.ncbigene" "miriam.kegg.pathway"
#> [4] "miriam.kegg.compound"
# Get all attribute names containing "miriam"
getAttribute(ex_kgml_sig, "miriam.ncbigene")
#> [[1]]
#> [1] "1435" "1942" "1943" "1944" "1945" "1946" "1950" "2246" "2247"
#> [10] "2248" "2249" "2250" "2251" "2252" "2253" "2254" "2255" "2256"
#> [19] "2257" "2258" "2259" "2277" "26281" "26291" "27006" "284" "285"
#> [28] "3082" "3479" "3630" "4254" "4803" "51378" "5154" "5155" "5228"
#> [37] "56034" "7422" "7423" "7424" "80310" "8074" "8817" "8822" "8823"
#> [46] "9965"
#>
#> [[2]]
#> [1] "1436" "1956" "1969" "2260" "2261" "2263" "2264" "2321" "2324" "3480"
#> [11] "3643" "3791" "3815" "4233" "4804" "5156" "5159" "7010"
#>
#> [[3]]
#> [1] "25759" "399694" "53358" "6464"
#>
#> [[4]]
#> [1] "2885"
#>
#> [[5]]
#> [1] "2549" "9846"
#>
#> [[6]]
#> [1] "5781"
#>
#> [[7]]
#> [1] "6654" "6655"
#>
#> [[8]]
#> [1] "22800" "22808" "3265" "3845" "4893" "6237"
#>
#> [[9]]
#> [1] "7535"
#>
#> [[10]]
#> [1] "27040"
#>
#> [[11]]
#> [1] "5335" "5336"
#>
#> [[12]]
#> NULL
#>
#> [[13]]
#> [1] "10125" "10235" "115727" "25780"
#>
#> [[14]]
#> [1] "3363"
#>
#> [[15]]
#> [1] "10681" "2782" "2783" "2784" "2785" "2786" "2787" "2788"
#> [9] "2790" "2791" "2792" "2793" "51764" "54331" "55970" "59345"
#> [17] "648044" "94235"
#>
#> [[16]]
#> [1] "5923" "5924"
#>
#> [[17]]
#> NULL
#>
#> [[18]]
#> NULL
#>
#> [[19]]
#> [1] "5566" "5567" "5568" "5613"
#>
#> [[20]]
#> [1] "163688" "51806" "801" "805" "808" "810"
#>
#> [[21]]
#> NULL
#>
#> [[22]]
#> NULL
#>
#> [[23]]
#> [1] "4763"
#>
#> [[24]]
#> [1] "100271927" "10156" "22821" "5921" "5922" "64926"
#> [7] "8437" "8831" "9462"
#>
#> [[25]]
#> [1] "11186"
#>
#> [[26]]
#> [1] "6789"
#>
#> [[27]]
#> [1] "83593"
#>
#> [[28]]
#> [1] "7074"
#>
#> [[29]]
#> [1] "23533" "5290" "5291" "5293" "5294" "5295" "5296" "8503"
#>
#> [[30]]
#> [1] "4301"
#>
#> [[31]]
#> [1] "5894"
#>
#> [[32]]
#> [1] "5900"
#>
#> [[33]]
#> [1] "23179"
#>
#> [[34]]
#> [1] "5863"
#>
#> [[35]]
#> [1] "51196"
#>
#> [[36]]
#> [1] "9610"
#>
#> [[37]]
#> [1] "10928"
#>
#> [[38]]
#> [1] "8315"
#>
#> [[39]]
#> [1] "9771"
#>
#> [[40]]
#> [1] "5879" "5880" "5881"
#>
#> [[41]]
#> [1] "10298" "5058" "5062" "5063" "56924" "57144"
#>
#> [[42]]
#> [1] "387"
#>
#> [[43]]
#> NULL
#>
#> [[44]]
#> [1] "10000" "207" "208"
#>
#> [[45]]
#> [1] "1147" "3551" "8517"
#>
#> [[46]]
#> [1] "4790" "5970"
#>
#> [[47]]
#> [1] "572"
#>
#> [[48]]
#> [1] "598"
#>
#> [[49]]
#> [1] "4303"
#>
#> [[50]]
#> [1] "356"
#>
#> [[51]]
#> [1] "5604" "5605"
#>
#> [[52]]
#> [1] "5594" "5595"
#>
#> [[53]]
#> [1] "100137049" "11145" "123745" "255189" "26279" "283748"
#> [7] "30814" "391013" "50487" "51365" "5319" "5320"
#> [13] "5321" "5322" "64600" "81579" "8398" "8399"
#> [19] "84647" "8605" "8681"
#>
#> [[54]]
#> [1] "2002"
#>
#> [[55]]
#> [1] "2113" "2114"
#>
#> [[56]]
#> [1] "8844"
#>
#> [[57]]
#> [1] "5906" "5908"
#>
#> [[58]]
#> [1] "5898" "5899"
#>
#> [[59]]
#> [1] "5599" "5601" "5602"
#>
#> [[60]]
#> [1] "55770"
#>
#> [[61]]
#> [1] "29110"
#>
#> [[62]]
#> [1] "5966"
#>
#> [[63]]
#> [1] "5337" "5338"
#>
#> [[64]]
#> [1] "998"
#>
#> [[65]]
#> [1] "5578" "5579" "5582"
#>
#> [[66]]
#> [1] "25" "27"
#>
#> [[67]]
#> [1] "5868" "5869" "5878"
#>
#> [[68]]
#> [1] "382"
#>
#> [[69]]
#> [1] "5879"
#>
#> [[70]]
#> [1] "6654"
#>
#> [[71]]
#> [1] "3265" "3845" "4893"
#>
#> [[72]]
#> [1] "22808"
#>
#> [[73]]
#> [1] "5923"
#>
#> [[74]]
#> [1] "6237"
#>
#> [[75]]
#> NULL
#>
#> [[76]]
#> [1] "10344" "10563" "10850" "2919" "2920" "2921" "3576" "3627"
#> [9] "388372" "414062" "4283" "5196" "5197" "5473" "56477" "58191"
#> [17] "6346" "6347" "6348" "6349" "6351" "6352" "6354" "6355"
#> [25] "6356" "6357" "6358" "6359" "6360" "6361" "6362" "6363"
#> [33] "6364" "6366" "6367" "6368" "6369" "6370" "6372" "6373"
#> [41] "6374" "6375" "6376" "6387" "6846" "9547" "9560"
#>
#> [[77]]
#> [1] "10663" "10803" "1230" "1232" "1233" "1234" "1235" "1236"
#> [9] "1237" "1524" "2826" "2829" "2833" "3577" "3579" "643"
#> [17] "729230" "7852"
#>
#> [[78]]
#> [1] "3717" "3718"
#>
#> [[79]]
#> [1] "6772" "6773" "6774" "6777"
#>
#> [[80]]
#> [1] "2770" "2771" "2773"
#>
#> [[81]]
#> [1] "107" "108" "109" "111" "112" "113" "114" "115"
#> [9] "196883"
#>
#> [[82]]
#> [1] "2268" "3055" "4067" "6714"
#>
#> [[83]]
#> [1] "5894" "673"
#>
#> [[84]]
#> [1] "5604"
#>
#> [[85]]
#> [1] "5590"
#>
#> [[86]]
#> [1] "4792" "4793"
#>
#> [[87]]
#> [1] "2931" "2932"
#>
#> [[88]]
#> [1] "3702"
#>
#> [[89]]
#> [1] "10451" "7409" "7410"
#>
#> [[90]]
#> [1] "5879" "5880"
#>
#> [[91]]
#> [1] "5058"
#>
#> [[92]]
#> [1] "7454" "8976"
#>
#> [[93]]
#> [1] "6093" "9475"
#>
#> [[94]]
#> [1] "57580"
#>
#> [[95]]
#> [1] "" "9844" "1794"
#>
#> [[96]]
#> [1] "2185"
#>
#> [[97]]
#> [1] "5829"
#>
#> [[98]]
#> [1] "1398" "1399"
#>
#> [[99]]
#> [1] "5747"
#>
#> [[100]]
#> [1] "9564"
#>
#> [[101]]
#> [1] "23236" "5330" "5331" "5332"
#>
#> [[102]]
#> [1] "10235"
#>
#> [[103]]
#> [1] "" "56288" "5590" "7074"
#>
#> [[104]]
#> [1] "5579" "5580"
#>
#> [[105]]
#> [1] "653361"
#>
#> [[106]]
#> [1] "408" "409"
#>
#> [[107]]
#> [1] "131890" "156" "157" "2868" "2869" "2870" "6011"
#>
#> [[108]]
#> [1] "2309"
#>
# Remove an attribute from graph
graph <- rmAttribute(ex_kgml_sig, "miriam.ncbigene")