Network plot for analyzing and visualizing relationship of genes.

Usage

network_plot(
  data,
  calc_by = "degree",
  degree_value = 0.5,
  normal_color = "#008888cc",
  border_color = "#FFFFFF",
  from_color = "#FF0000cc",
  to_color = "#008800cc",
  normal_shape = "circle",
  spatial_shape = "circle",
  node_size = 25,
  lable_color = "#FFFFFF",
  label_size = 0.5,
  edge_color = "#888888",
  edge_width = 1.5,
  edge_curved = TRUE,
  net_layout = "layout_on_sphere"
)

Arguments

data: Dataframe: Network data from WGCNA tan module top-200 dataframe (1st-col: Source, 2nd-col: Target).
calc_by: Character: calculate relationship by "degree", "node". Default: "degree".
degree_value: Numeric: degree value when calc_by = "degree". Default: 0.05, min: 0.00, max: 1.00.
normal_color: Character: normal relationship nodes color (color name of hex value).
border_color: Character: node border color (color name or hex value).
from_color: Character: the start color of nodes that meet degree_value.
to_color: Character: the end color of nodes that meet degree_value.
normal_shape: Character: normal node shape. Default: "circle", options: "circle", "crectangle", "csquare", "none", "pie", "raster", "rectangle", "sphere", "square", "vrectangle".
spatial_shape: Character: meet degree_value node shape. Default: "csquare", options: "circle", "crectangle", "csquare", "none", "pie", "raster", "rectangle", "sphere", "square", "vrectangle".
node_size: Numeric: node size. Default: 10, min: 0, max: NULL.
lable_color: Character: gene labels color. Default: "#FFFFFF".
label_size: Numeric: node label size. Default: 0.5, min: 0, max: NULL.
edge_color: Character: edges color. Default: "#888888".
edge_width: Numeric: edges width. Default: 1.5.
edge_curved: Logical: curved edges. Default: TRUE, options: TRUE, FALSE.
net_layout: Character: network layout. Default: "layout_on_sphere", options: "layout_as_bipartite", "layout_as_star", "layout_as_tree", "layout_components", "layout_in_circle", "layout_nicely", "layout_on_grid", "layout_on_sphere","layout_randomly","layout_with_dh","layout_with_drl","layout_with_fr","layout_with_gem","layout_with_graphopt","layout_with_kk","layout_with_lgl","layout_with_mds","layout_with_sugiyama".

Value

Plot: network plot for analyzing and visualizing relationship of genes.

Author

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(network_data)
head(network_data)
#>   Source Target
#> 1  Cebpd  Cebpd
#> 2  CYR61  Cebpd
#> 3  Cebpd CDKN1B
#> 4  CYR61 CDKN1B
#> 5   junb  Cebpd
#> 6 IGFBP1  Cebpd

# 3. Default parameters
network_plot(network_data)
#> Warning: number of items to replace is not a multiple of replacement length


# 4. Set calc_by = "node"
network_plot(network_data, calc_by = "node")


# 5. Set degree_value = 0.1
network_plot(network_data, degree_value = 0.1)
#> Warning: number of items to replace is not a multiple of replacement length


# 6. Set normal_color = "#ff8800cc"
network_plot(network_data, normal_color = "#ff8800cc")
#> Warning: number of items to replace is not a multiple of replacement length


# 7. Set net_layout = "layout_as_tree"
network_plot(network_data, net_layout = "layout_as_tree")
#> Warning: number of items to replace is not a multiple of replacement length