## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) library(CIMICE) library(dplyr) library(igraph) library(Matrix) library(purrr) ## ----cars, results=FALSE------------------------------------------------------ # read from file read_CAPRI(system.file("extdata", "example.CAPRI", package = "CIMICE", mustWork = TRUE)) ## ----------------------------------------------------------------------------- # from a string read_CAPRI_string(" s\\g A B C D S1 0 0 0 1 S2 1 0 0 0 S3 1 0 0 0 S4 1 0 0 1 S5 1 1 0 1 S6 1 1 0 1 S7 1 0 1 1 S8 1 1 0 1 ") ## ----------------------------------------------------------------------------- # using CIMICE::make_dataset and CIMICE::update_df # genes make_dataset(A,B,C,D) %>% # samples update_df("S1", 0, 0, 0, 1) %>% update_df("S2", 1, 0, 0, 0) %>% update_df("S3", 1, 0, 0, 0) %>% update_df("S4", 1, 0, 0, 1) %>% update_df("S5", 1, 1, 0, 1) %>% update_df("S6", 1, 1, 0, 1) %>% update_df("S7", 1, 0, 1, 1) %>% update_df("S8", 1, 1, 0, 1) ## ----------------------------------------------------------------------------- preproc <- dataset_preprocessing(example_dataset()) samples <- preproc[["samples"]] freqs <- preproc[["freqs"]] labels <- preproc[["labels"]] genes <- preproc[["genes"]] ## ----------------------------------------------------------------------------- g <- graph_non_transitive_subset_topology(samples,labels) ## ----echo=FALSE--------------------------------------------------------------- V(g)$vertex.size <- rep(10, length(V(g))) plot(g, vertex.size=rep(55, length(V(g)))) ## ----------------------------------------------------------------------------- W <- compute_weights_default(g, freqs) ## ----------------------------------------------------------------------------- out <- quick_run(example_dataset()) # quick_run summarizes all the previous steps draw_visNetwork(out)