Assess the quality of each network generated by SJARACNe

This function is used to assess the quality of networks generated by SJARACNe. It returns a summary table of key statistics of networks. The users can also generate the html quality control report by turning generate_html = TRUE.

Usage

drawNetworkQC(
  network_file = NULL,
  sjaracne_dir = NULL,
  directed = TRUE,
  weighted = TRUE,
  generate_html = TRUE,
  outdir = NULL,
  prefix = NULL
)

Arguments

network_file: The path to the network file (consensus_network_ncol_.txt) for quality control
sjaracne_dir: The path to the folder of SJARACNe runs. When this argument is given, scMINER will automatically retrieve all network files (consensus_network_ncol_.txt) in this folder and generate quality control report for all of them.
directed: Logical, whether the network is directed or not. All networks generated by SJARACNe are directed. Default: TRUE.
weighted: Logical, whether the edges of the network is weighted or not. All networks generated by SJARACNe are weighted by mutual information ("MI" column). Default: TRUE.
generate_html: Logical, whether to generate a html report. Default: TRUE.
outdir: Character or NULL, the path to save the html report. If NULL, the html report will be saved in the same folder of the network file. Default: NULL. Ignored if generate_html = FALSE.
prefix: Character or NULL, the character string to add in front of the html report file name. Default: NULL. Ignored if generate_html = FALSE.

Value

This function will print the statistics of several key quality metrics of network(s). If generate_html is set TRUE, it also generates a html file of quality control report and save it to the same folder of the network file (by default) or the folder specified by "outdir".

Examples

if (FALSE) { # \dontrun{
## 1. Assess the quality of network from network files
drawNetworkQC(network_file = "/project_space/SJARACNE/B/SIG/b100/consensus_network_ncol_.txt", generate_html = TRUE,
              outdir = "/folder-to-save-report_file", prefix = "PBMC14")

## 2. Assess the quality of network from the directory of network files
drawNetworkQC(sjaracne_dir = "/project_space/SJARACNE", generate_html = TRUE)
} # }