plot_gene_group: Plot a module

Description Usage Arguments Value Examples

View source: R/plot_utils.R

Description

Plot the regulators module and heatmap of the expression inferred downstream genes for each sample. It can be interpreted as two parts: the bars at the top shows how samples are splited by the regression tree and the heatmap at the bottom shows how downstream genes are regulated by each subgroup determined by the regulators.

Usage

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plot_gene_group(
  gnet_result,
  group_idx,
  tree_layout = 1,
  max_gene_num = 100,
  plot_leaf_labels = TRUE,
  group_labels = NULL
)

Arguments

gnet_result

Results returned by gnet().

group_idx

Index of the module.

tree_layout

zoom ratio for the regulatory tree. Default is 1. Need to be increased for trees with >5 regulators.

max_gene_num

Max size of gene to plot in the heatmap. Only genes with highest n variances will be kept.

plot_leaf_labels

If the plot includes a color bar of leaf labels at the bottom.

group_labels

Labels of experiment conditions,Used for the color bar of experiment conditions. Default is NULL

Value

None

Examples

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set.seed(1)
init_group_num = 5
init_method = 'boosting'
exp_data <- matrix(rnorm(50*10),50,10)
reg_names <- paste0('TF',1:5)
rownames(exp_data) <- c(reg_names,paste0('gene',1:(nrow(exp_data)-length(reg_names))))
colnames(exp_data) <- paste0('condition_',1:ncol(exp_data))
se <- SummarizedExperiment::SummarizedExperiment(assays=list(counts=exp_data))
gnet_result <- gnet(se,reg_names,init_method,init_group_num)
plot_gene_group(gnet_result,group_idx=1)

GNET2 documentation built on Nov. 8, 2020, 8:03 p.m.