runCondor: Turn PANDA network into a CONDOR object

In twangxxx/netZoo: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA into one workflow.

Description

CONDOR (COmplex Network Description Of Regulators) implements methods for clustering biapartite networks and estimatiing the contribution of each node to its community's modularity, [(Platig et al. 2016)]) This function uses the result of PANDA algorithm as the input dataset to run CONDOR algorithm. More about condor package and usage.

Usage

runCondor(df, threshold = m)

Arguments

df	Data Frame indicating the result of PANDA regulatory network, created by runPanda
threshold	Numeric vector of the customered threshold to select edges. Default value is the the midpoint between the median edge-weight of prior ( 3rd column "Motif" is 1.0) edges and the median edge-weight of non-prior edges (3rd column "Motif" is 0.0) in PANDA network, see calculateThreshold.

Value

a CONDOR object, see create.condor.object.

Examples

# refer to four input datasets files in inst/extdat
treated_expression_file_path <- system.file("extdata", "expr4.txt", package = "netZoo", mustWork = TRUE)
control_expression_file_path <- system.file("extdata", "expr10.txt", package = "netZoo", mustWork = TRUE)
motif_file_path <- system.file("extdata", "chip.txt", package = "netZoo", mustWork = TRUE)
ppi_file_path <- system.file("extdata", "ppi.txt", package = "netZoo", mustWork = TRUE)


# Run PANDA for treated and control network
treated_all_panda_result <- runPanda(e = treated_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )
control_all_panda_result <- runPanda(e = control_expression_file_path, m = motif_file_path, ppi = ppi_file_path, rm_missing = TRUE )

# access PANDA regulatory network
treated_net <- treated_all_panda_result$panda
control_net <- control_all_panda_result$panda

# Run CONDOR
treated_condor_object <- runCondor(treated_net, threshold = 0)
control_condor_object <- runCondor(control_net, threshold = 0)

# plot communities
# package igraph and package viridisLite are already loaded with this package.

treated_color_num <- max(treated_condor_object$red.memb$com)
treated_color <- viridis(treated_color_num, alpha = 1, begin = 0, end = 1, direction = 1, option = "D")
condor.plot.communities(treated_condor_object, color_list=treated_color, point.size=0.04, xlab="Target", ylab="Regulator")

control_color_num <- max(control_condor_object$red.memb$com)
control_color <- viridis(control_color_num, alpha = 1, begin = 0, end = 1, direction = 1, option = "D")
condor.plot.communities(control_condor_object, color_list=control_color , point.size=0.04, xlab="Target", ylab="Regulator")

twangxxx/netZoo documentation built on May 17, 2019, 1:02 p.m.