In ficusss/Pagoda2GraphImprovement:

title: "Demonstration 2" output: html_document: toc: true html_notebook: default

---

Подключаем требуемые пакеты

library(igraph)
library(pagoda2)
library(ggplot2)
#library(magrittr)
library(pbapply)

theme_set(theme_bw())

set.seed(2018)

Меняем PCA

path_floder <- DataPath("GSE109447_13055_cm.rds")

load_matrix <- readRDS(path_floder)
load_matrix <- load_matrix[!duplicated(rownames(load_matrix)),]

p2 <- pagoda2::basicP2proc(load_matrix, n.cores=10)

Уточнение произведенное по кластеризации multilevel

p2up <- UpdatePagoda(primary.data = load_matrix, pagoda.obj = p2, clustering.type = 'multilevel',
                      k = c(30), n.cores = 25, embeding.type = 'largeVis')

p2up$getKnnClusters(method = igraph::infomap.community, type = "PCA", name = "infomap")

Validation

conos::embeddingPlot(p2$embeddings$PCA$tSNE, groups=p2$clusters$PCA$multilevel)
conos::embeddingPlot(p2$embeddings$PCA$tSNE, groups=p2$clusters$PCA$infomap)
conos::embeddingPlot(p2$embeddings$PCA$tSNE, groups=p2up$clusters$PCA$infomap)

conos::embeddingPlot(p2$embeddings$PCA$largeVis, groups=p2$clusters$PCA$infomap)
conos::embeddingPlot(p2up$embeddings$PCA$largeVis,
                     groups=p2$clusters$PCA$infomap)

conos::embeddingPlot(p2$embeddings$PCA$largeVis,
                     groups=p2up$clusters$PCA$infomap)
conos::embeddingPlot(p2up$embeddings$PCA$largeVis,
                     groups=p2up$clusters$PCA$infomap)

ficusss/Pagoda2GraphImprovement documentation built on May 8, 2019, 8:58 p.m.