NetViz.RdVisualization for Enhancer-Gene Network.
NetViz( inte.res, type, whole = TRUE, gene = NULL, peak = NULL, labels = NULL, show.all.labels = FALSE, seed = 1000, edge.width = 0.6, edge.color = "black", edge.alpha = 0.8, node.size = 3, node.color = c("red", "blue"), node.alpha = 0.5, node.label.size = 2.5, node.label.color = "navy", node.label.len = 0.5 )
| inte.res | Dataframe contains integrated results. |
|---|---|
| type | The type of integrated results ("Type" column of |
| whole | Logical value, whether to visualize all interactions. Default: TRUE. |
| gene | Genes used to extract subset of the whole network. Default: NULL. |
| peak | Peaks used to extract subset of the whole network. Default: NULL. |
| labels | Genes/Peaks used to label on the plot. Default: NULL. |
| show.all.labels | Logical value, whether to show all labels, useful when extracting subset of the whole network. Default: FALSE. |
| seed | Seed. |
| edge.width | The width of the edge. Default: 0.6. |
| edge.color | The color of the edge. Default: "black". |
| edge.alpha | The alpha of the edge. Default: 0.8. |
| node.size | The size of the node. Default: 3. |
| node.color | The color vector for enhancer and gene. Default: c("red", "blue"). |
| node.alpha | The alpha of the node color. Default: 0.6. |
| node.label.size | The size of the node label. Default: 2.5. |
| node.label.color | The color of the node label. Default: "navy". |
| node.label.len | The line length of the node label. Default: 0.5. |
A ggplot2 object.
# # whole network # NetViz(inte.res = test, whole = TRUE, type = "Up_Up", # labels = c("Ripor2", "C4b", "Ccl12", "Fcgr2b", "Ly86", "Ccl5", "Ccr5"), seed = 1001) # # subset with gene and peak # NetViz(inte.res = test, whole = FALSE, type = "Up_Up", # gene = c("Ripor2", "C4b", "Ccl12", "Fcgr2b", "Ly86", "Ccl5", "Ccr5"), # peak = c("15:74931074-74931694|Ly6e|P", "9:124012191-124012495|Ccr3|P", "7:141122254-141122774|Ptdss2|P", "1:170985190-170986301|Fcgr2b|P"), # show.all.labels = TRUE, seed = 1001) # # single gene # NetViz(inte.res = test, whole = FALSE, type = "Up_Up", # gene = c("Ripor2", "C4b", "Ccl12", "Fcgr2b", "Ly86", "Ccl5", "Ccr5"), # show.all.labels = TRUE, seed = 1001) # # single peak # NetViz(inte.res = test, whole = FALSE, type = "Up_Up", # peak = c("15:74931074-74931694|Ly6e|P", "9:124012191-124012495|Ccr3|P", "7:141122254-141122774|Ptdss2|P", "1:170985190-170986301|Fcgr2b|P"), # show.all.labels = TRUE, seed = 1001)