Description Usage Arguments Details Value References See Also Examples
Build an interactive heatmap of the common GO terms frequency between several partitions.
1 2 3 4 | compare_clusters(clusters)
## S4 method for signature 'list'
compare_clusters(clusters)
|
clusters |
a |
Build an interactive heatmap of common GO terms frequency between partitions from several
GO_clusters-class
objects.
an interactive javascript heatmap.
Carson Sievert, Chris Parmer, Toby Hocking, Scott Chamberlain, Karthik Ram, Marianne Corvellec and Pedro Despouy (2017). plotly: Create Interactive Web Graphics via 'plotly.js'. R package version 4.6.0. https://CRAN.R-project.org/package=plotly
Other GO_clusters: GO_clusters-class
,
GOclusters_heatmap
,
clusters_cor
, show_heatmap
,
show_table
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 | ###################
# load example object
data(
myGOs,
package="ViSEAGO"
)
## Not run:
###################
# compute Semantic Similarity (SS)
myGOs<-ViSEAGO::compute_SS_distances(
myGOs,
distance=c("Resnik","Lin","Rel","Jiang","Wang")
)
##################
# Resnik distance GO terms heatmap
Resnik_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showGOlabels=TRUE,
GO.tree=list(
tree=list(
distance="Resnik",
aggreg.method="ward.D2"
),
cut=list(
dynamic=list(
deepSplit=2,
minClusterSize =2
)
)
),
samples.tree=NULL
)
##################
# Lin distance GO terms heatmap
Lin_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showGOlabels=TRUE,
GO.tree=list(
tree=list(
distance="Lin",
aggreg.method="ward.D2"
),
cut=list(
dynamic=list(
deepSplit=2,
minClusterSize =2
)
)
),
samples.tree=NULL
)
##################
# Resnik distance GO terms heatmap
Rel_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showGOlabels=TRUE,
GO.tree=list(
tree=list(
distance="Rel",
aggreg.method="ward.D2"
),
cut=list(
dynamic=list(
deepSplit=2,
minClusterSize =2
)
)
),
samples.tree=NULL
)
##################
# Resnik distance GO terms heatmap
Jiang_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showGOlabels=TRUE,
GO.tree=list(
tree=list(
distance="Jiang",
aggreg.method="ward.D2"
),
cut=list(
dynamic=list(
deepSplit=2,
minClusterSize =2
)
)
),
samples.tree=NULL
)
##################
# Resnik distance GO terms heatmap
Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showGOlabels=TRUE,
GO.tree=list(
tree=list(
distance="Wang",
aggreg.method="ward.D2"
),
cut=list(
dynamic=list(
deepSplit=2,
minClusterSize =2
)
)
),
samples.tree=NULL
)
## End(Not run)
###################
# clusters to compare
clusters<-list(
Resnik="Resnik_clusters_wardD2",
Lin="Lin_clusters_wardD2",
Rel="Rel_clusters_wardD2",
Jiang="Jiang_clusters_wardD2",
Wang="Wang_clusters_wardD2"
)
## Not run:
###################
# clusters content comparisons
clusters_comp<-ViSEAGO::compare_clusters(clusters)
## End(Not run)
|
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