add to networks tutorial

drieslab · Oct 25, 2024 · 2f84eef · 2f84eef
1 parent a4e85fe
commit 2f84eef
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diff --git a/vignettes/networks.Rmd b/vignettes/networks.Rmd
@@ -178,6 +178,82 @@ dimPlot2D(mer, show_NN_network = TRUE, nn_network_to_use = "kNN", network_name =
 knitr::include_graphics("images/networks/5_kNN_dim.png")
 ```
 
+
+# API function
+
+`createNetwork()` exported from *GiottoClass* allows creation of any of the above network types, starting from a `matrix` of nodes. These nodes can be n-dimensional expression information, dimension reduction, or spatial coordinates. The output is either `igraph` if `as.igraph = TRUE` and `data.table` otherwise.
+
+```{r, eval=FALSE}
+topo <- expand.grid(x = 1:nrow(volcano),
+                    y = 1:ncol(volcano))
+topo$z <- c(volcano)
+topo <- as.matrix(topo)
+
+createNetwork(topo, type = "kNN", k = 8) # returns as igraph
+```
+
+```
+IGRAPH 64720af DNW- 5307 42456 -- 
++ attr: name (v/c), weight (e/n), distance (e/n)
++ edges from 64720af (vertex names):
+ [1] 1 ->88  2 ->89  3 ->90  4 ->91  5 ->92  6 ->7   7 ->6   8 ->94  9 ->95  10->97  11->97 
+[12] 12->99  13->12  14->13  15->102 16->102 17->103 18->19  19->18  20->21  21->22  22->21 
+[23] 23->24  24->25  25->26  26->25  27->115 28->29  29->28  30->31  31->30  32->31  33->120
+[34] 34->121 35->36  36->124 37->38  38->37  39->40  40->41  41->40  42->43  43->42  44->45 
+[45] 45->46  46->45  47->134 48->49  49->48  50->51  51->52  52->51  53->52  54->141 55->56 
+[56] 56->57  57->56  58->59  59->60  60->59  61->62  62->63  63->62  64->65  65->64  66->67 
+[67] 67->66  68->69  69->68  70->69  71->158 72->159 73->160 74->161 75->162 76->163 77->165
+[78] 78->79  79->78  80->81  81->80  82->83  83->170 84->85  85->172 86->87  87->86  88->1  
++ ... omitted several edges
+```
+
+```{r, eval=FALSE}
+createNetwork(topo, type = "kNN", k = 8, as.igraph = FALSE) # return as data.table
+```
+
+```
+        from    to    weight distance
+       <int> <int>     <num>    <num>
+    1:     1    88 0.5000000 1.000000
+    2:     2    89 0.5000000 1.000000
+    3:     3    90 0.5000000 1.000000
+    4:     4    91 0.5000000 1.000000
+    5:     5    92 0.5000000 1.000000
+   ---                               
+42452:  5303  5130 0.3090170 2.236068
+42453:  5304  5306 0.3333333 2.000000
+42454:  5305  5303 0.3333333 2.000000
+42455:  5306  5131 0.3090170 2.236068
+42456:  5307  5131 0.2612039 2.828427
+```
+
+```{r, eval=FALSE}
+# default weight for kNN was 1 / (d + 1)
+# use a custom weight function
+createNetwork(topo,
+    type = "kNN", 
+    k = 8, 
+    as.igraph = FALSE,
+    weight_fun = function(d) 1 / (d)^2
+)
+```
+
+```
+        from    to weight distance
+       <int> <int>  <num>    <num>
+    1:     1    88  1.000 1.000000
+    2:     2    89  1.000 1.000000
+    3:     3    90  1.000 1.000000
+    4:     4    91  1.000 1.000000
+    5:     5    92  1.000 1.000000
+   ---                            
+42452:  5303  5130  0.200 2.236068
+42453:  5304  5306  0.250 2.000000
+42454:  5305  5303  0.250 2.000000
+42455:  5306  5131  0.200 2.236068
+42456:  5307  5131  0.125 2.828427
+```
+
 # Session Info
 ```{r, eval=FALSE}
 sessionInfo()