plot_network_heatmap: Plot network heatmap

In inferCSN: Inferring Cell-Specific Gene Regulatory Network

Plot network heatmap

Description

Plot network heatmap

Usage

plot_network_heatmap(
  network_table,
  regulators = NULL,
  targets = NULL,
  switch_matrix = TRUE,
  show_names = FALSE,
  heatmap_size_lock = TRUE,
  heatmap_size = 5,
  heatmap_height = NULL,
  heatmap_width = NULL,
  heatmap_title = NULL,
  heatmap_color = c("#1966ad", "white", "#bb141a"),
  border_color = "gray",
  rect_color = NA,
  anno_width = 1,
  anno_height = 1,
  row_anno_type = NULL,
  column_anno_type = NULL,
  legend_name = "Weight",
  row_title = "Regulators"
)

Arguments

network_table	The weight data table of network.
regulators	Regulators list.
targets	Targets list.
switch_matrix	Logical value, default is TRUE, whether to weight data table to matrix.
show_names	Logical value, default is FALSE, whether to show names of row and column.
heatmap_size_lock	Lock the size of heatmap.
heatmap_size	Default is 5. The size of heatmap.
heatmap_height	The height of heatmap.
heatmap_width	The width of heatmap.
heatmap_title	The title of heatmap.
heatmap_color	Colors of heatmap.
border_color	Default is gray. Color of heatmap border.
rect_color	Default is NA. Color of heatmap rect.
anno_width	Width of annotation.
anno_height	Height of annotation.
row_anno_type	Default is NULL, could add a annotation plot to row, choose one of boxplot, barplot, histogram, density, lines, points, and horizon.
column_anno_type	Default is NULL, could add a annotation plot to column, choose one of boxplot, barplot, histogram, density, lines, and points.
legend_name	The name of legend.
row_title	The title of row.

Value

A heatmap

Examples

data("example_matrix")
data("example_ground_truth")
network_table <- inferCSN(example_matrix)

p1 <- plot_network_heatmap(
  example_ground_truth[, 1:3],
  heatmap_title = "Ground truth",
  legend_name = "Ground truth"
)
p2 <- plot_network_heatmap(
  network_table,
  heatmap_title = "inferCSN",
  legend_name = "inferCSN"
)
ComplexHeatmap::draw(p1 + p2)

p3 <- plot_network_heatmap(
  network_table,
  heatmap_title = "inferCSN",
  legend_name = "Weight1",
  heatmap_color = c("#20a485", "#410054", "#fee81f")
)
p4 <- plot_network_heatmap(
  network_table,
  heatmap_title = "inferCSN",
  legend_name = "Weight2",
  heatmap_color = c("#20a485", "white", "#fee81f")
)
ComplexHeatmap::draw(p3 + p4)

plot_network_heatmap(
  network_table,
  show_names = TRUE,
  rect_color = "gray90",
  row_anno_type = "density",
  column_anno_type = "barplot"
)

plot_network_heatmap(
  network_table,
  regulators = c("g1", "g2"),
  show_names = TRUE
)

plot_network_heatmap(
  network_table,
  targets = c("g1", "g2"),
  row_anno_type = "boxplot",
  column_anno_type = "histogram",
  show_names = TRUE
)

plot_network_heatmap(
  network_table,
  regulators = c("g1", "g3", "g5"),
  targets = c("g3", "g6", "g9"),
  show_names = TRUE
)

inferCSN documentation built on Sept. 11, 2024, 9:32 p.m.