Score from combined model: perDataPCA + multiPLIER
2019-12-05
suppressPackageStartupMessages({
library(SummarizedExperiment)
library(PLIER)
library(grid)
library(circlize)
library(ComplexHeatmap)
library(GenomicSuperSignature)
})
source('/data2/GenomicSuperSignature/R/sampleScoreHeatmap.R')
source('/data2/GenomicSuperSignature/R/validte.R')1 Load models
recount2PCAmodel = readRDS("/data2/Genomic_Super_Signature/multiPCA/data/avgLoadingRecount2.rds")
recount_KEGG_model = readRDS("/data2/Genomic_Super_Signature/PLIER/data/recount_KEGG_PLIER_model.RDS")2 Load test data
load("/data2/GenomicSuperSignature/data/TCGA_validationDatasets.rda")
exprs.mat.ov = assay(TCGA_validationDatasets[["OV"]])
exprs.mat.coad = assay(TCGA_validationDatasets[["COAD"]])
cm = intersect(rownames(exprs.mat.ov), rownames(exprs.mat.coad))
exprs.mat = cbind(exprs.mat.ov[cm, 1:5], exprs.mat.coad[cm, 1:5]) # assign score to only 5 samples 3 PLIER functions
PLIER::plotU(recount_KEGG_model, auc.cutoff = 0.9, fdr.cutoff = 0.01, top = 2)
4 multiPLIER functions
4.1 GetNewDataB
iso.b.matrix = GetNewDataB(exprs.mat = exprs.mat,
plier.model = recount_KEGG_model)
sampleScoreHeatmap(t(iso.b.matrix), "TCGA_RNAseq", "recount_KEGG_model",
show_column_names = FALSE,
show_row_names = TRUE,
row_names_gp = 7)
topInd = order(iso.b.matrix[,1], decreasing = TRUE)[1:5]
bottomInd = order(iso.b.matrix[,1])[1:5]
sampleScoreHeatmap(t(iso.b.matrix[c(topInd, bottomInd), 1]), colnames(iso.b.matrix)[1], "recount_KEGG_model",
show_column_names = TRUE,
show_row_names = TRUE,
column_names_gp = 10)
4.2 GetPathwayCoverage
- pathway: proportion of “covered” pathways
- lv: proportion of LVs that have pathways associated with them
- sig.pathway.by.lv: number of pathways “covered” / number of LVs
GetPathwayCoverage(recount_KEGG_model)## $pathway
## [1] 0.8590604
##
## $lv
## [1] 0.464467
##
## $sig.pathway.by.lv
## [1] 0.64974624.3 CalculateUSparsity
a vector of length ncol(plier.results$U) that contains the proportion of positive
(significant.only = FALSE) or significant (significant.only = TRUE) entries in each
column
prop.vector = CalculateUSparsity(recount_KEGG_model)
head(prop.vector)## LV1 LV2 LV3 LV4 LV5 LV6
## 0.30536913 0.11744966 0.11744966 0.10067114 0.09395973 0.060402684.4 EvalWrapper
EvalWrapper(recount_KEGG_model)5 GenomicSuperSignature functions
score = GenomicSuperSignature::calScore(exprs.mat, recount2PCAmodel)
sampleScoreHeatmap(score[[1]], "TCGA_RNAseq", "recount_PCA_model",
show_column_names = FALSE,
show_row_names = TRUE,
row_names_gp = 7)
x = t(score[[1]])
topInd = order(x[,1], decreasing = TRUE)[1:5]
bottomInd = order(x[,1])[1:5]
subset = x[c(topInd, bottomInd), 1]
sampleScoreHeatmap(t(subset), colnames(x)[1], "recount2_PCA_model",
show_column_names = TRUE,
show_row_names = TRUE,
column_names_gp = 10)
topPathways_recount2PCAmodel = readRDS("/data2/Genomic_Super_Signature/multiPCA/data/topPathways_recount2PCAmodel.rds")
topPathways_recount2PCAmodel[names(subset)]## Cl118_22 (44/44)
## Up_1 ECM-receptor interaction
## Up_2 Asthma
## Up_3 Staphylococcus aureus infection
## Up_4 Arrhythmogenic right ventricular cardiomyopathy (ARVC)
## Up_5 Complement and coagulation cascades
## Up_6 Malaria
## Up_7 Renin-angiotensin system
## Up_8 Protein digestion and absorption
## Up_9 Cell adhesion molecules (CAMs)
## Up_10 Mineral absorption
## Down_1 Ribosome
## Down_2 Protein processing in endoplasmic reticulum
## Down_3 Spliceosome
## Down_4 Primary immunodeficiency
## Down_5 N-Glycan biosynthesis
## Down_6 mRNA surveillance pathway
## Down_7 Proteasome
## Down_8 Aminoacyl-tRNA biosynthesis
## Down_9 NF-kappa B signaling pathway
## Down_10 B cell receptor signaling pathway
## Cl118_06 (31/31)
## Up_1 Regulation of actin cytoskeleton
## Up_2 Thyroid hormone signaling pathway
## Up_3 Focal adhesion
## Up_4 Phosphatidylinositol signaling system
## Up_5 MicroRNAs in cancer
## Up_6 Adherens junction
## Up_7 Cortisol synthesis and secretion
## Up_8 Axon guidance
## Up_9 Proteoglycans in cancer
## Up_10 Salivary secretion
## Down_1 Ribosome
## Down_2 Oxidative phosphorylation
## Down_3 Parkinson disease
## Down_4 Systemic lupus erythematosus
## Down_5 Huntington disease
## Down_6 Non-alcoholic fatty liver disease (NAFLD)
## Down_7 Proteasome
## Down_8 Cardiac muscle contraction
## Down_9 Alzheimer disease
## Down_10 Thermogenesis
## Cl118_108 (46/46)
## Up_1 Influenza A
## Up_2 Measles
## Up_3 Protein processing in endoplasmic reticulum
## Up_4 Osteoclast differentiation
## Up_5 Mitophagy
## Up_6 Prolactin signaling pathway
## Up_7 Hepatitis C
## Up_8 C-type lectin receptor signaling pathway
## Up_9 Collecting duct acid secretion
## Up_10 Focal adhesion
## Down_1 DNA replication
## Down_2 Homologous recombination
## Down_3 Fanconi anemia pathway
## Down_4 Mismatch repair
## Down_5 Base excision repair
## Down_6 Cell cycle
## Down_7 Nucleotide excision repair
## Down_8 Systemic lupus erythematosus
## Down_9 Drug metabolism
## Down_10 One carbon pool by folate
## Cl118_46 (37/37)
## Up_1 Steroid hormone biosynthesis
## Up_2 Chemical carcinogenesis
## Up_3 Metabolism of xenobiotics by cytochrome P450
## Up_4 Asthma
## Up_5 Ascorbate and aldarate metabolism
## Up_6 Necroptosis
## Up_7 TNF signaling pathway
## Up_8 Apoptosis
## Up_9 Rap1 signaling pathway
## Up_10 Serotonergic synapse
## Down_1 Gap junction
## Down_2 mRNA surveillance pathway
## Down_3 Citrate cycle (TCA cycle)
## Down_4 Fat digestion and absorption
## Down_5 Th17 cell differentiation
## Down_6 Vascular smooth muscle contraction
## Down_7 RNA transport
## Down_8 Aminoacyl-tRNA biosynthesis
## Down_9 Chronic myeloid leukemia
## Down_10 Oxytocin signaling pathway
## Cl118_74 (16/16)
## Up_1 Malaria
## Up_2 Rheumatoid arthritis
## Up_3 Staphylococcus aureus infection
## Up_4 Cytokine-cytokine receptor interaction
## Up_5 Antigen processing and presentation
## Up_6 Dilated cardiomyopathy (DCM)
## Up_7 ECM-receptor interaction
## Up_8 Complement and coagulation cascades
## Up_9 Hypertrophic cardiomyopathy (HCM)
## Up_10 Phagosome
## Down_1 Proximal tubule bicarbonate reclamation
## Down_2 Mineral absorption
## Down_3 Peroxisome
## Down_4 Histidine metabolism
## Down_5 Glycerolipid metabolism
## Down_6 Glycine, serine and threonine metabolism
## Down_7 PPAR signaling pathway
## Down_8 Pyruvate metabolism
## Down_9 Glycolysis / Gluconeogenesis
## Down_10 Fructose and mannose metabolism
## Cl118_30 (26/26)
## Up_1 Proteasome
## Up_2 Ribosome
## Up_3 Oxidative phosphorylation
## Up_4 Parkinson disease
## Up_5 Spliceosome
## Up_6 Steroid biosynthesis
## Up_7 Pyruvate metabolism
## Up_8 Propanoate metabolism
## Up_9 Huntington disease
## Up_10 Ribosome biogenesis in eukaryotes
## Down_1 ABC transporters
## Down_2 Taste transduction
## Down_3 Graft-versus-host disease
## Down_4 African trypanosomiasis
## Down_5 Intestinal immune network for IgA production
## Down_6 Autoimmune thyroid disease
## Down_7 Allograft rejection
## Down_8 Staphylococcus aureus infection
## Down_9 Linoleic acid metabolism
## Down_10 Mitophagy
## Cl118_64 (48/48)
## Up_1 Ribosome
## Up_2 Oxidative phosphorylation
## Up_3 Parkinson disease
## Up_4 Huntington disease
## Up_5 Proteasome
## Up_6 Alzheimer disease
## Up_7 Cardiac muscle contraction
## Up_8 Non-alcoholic fatty liver disease (NAFLD)
## Up_9 Glycolysis / Gluconeogenesis
## Up_10 Thermogenesis
## Down_1 JAK-STAT signaling pathway
## Down_2 Herpes simplex virus 1 infection
## Down_3 Thyroid hormone signaling pathway
## Down_4 Phosphatidylinositol signaling system
## Down_5 Hepatitis B
## Down_6 Signaling pathways regulating pluripotency of stem cells
## Down_7 ECM-receptor interaction
## Down_8 Fanconi anemia pathway
## Down_9 MicroRNAs in cancer
## Down_10 Type II diabetes mellitus
## Cl118_86 (33/33)
## Up_1 Galactose metabolism
## Up_2 Lysosome
## Up_3 Endocrine and other factor-regulated calcium reabsorption
## Up_4 Bile secretion
## Up_5 Citrate cycle (TCA cycle)
## Up_6 N-Glycan biosynthesis
## Up_7 Starch and sucrose metabolism
## Up_8 Fructose and mannose metabolism
## Up_9 Autophagy
## Up_10 Insulin resistance
## Down_1 Autoimmune thyroid disease
## Down_2 Graft-versus-host disease
## Down_3 Allograft rejection
## Down_4 Legionellosis
## Down_5 Asthma
## Down_6 Type I diabetes mellitus
## Down_7 Staphylococcus aureus infection
## Down_8 Linoleic acid metabolism
## Down_9 Epstein-Barr virus infection
## Down_10 Apelin signaling pathway
## Cl118_94 (36/36)
## Up_1 Ribosome
## Up_2 Tyrosine metabolism
## Up_3 Pentose phosphate pathway
## Up_4 Phenylalanine metabolism
## Up_5 Fructose and mannose metabolism
## Up_6 Glycolysis / Gluconeogenesis
## Up_7 Galactose metabolism
## Up_8 Basal cell carcinoma
## Up_9 Fat digestion and absorption
## Up_10 Glutathione metabolism
## Down_1 Fanconi anemia pathway
## Down_2 RNA transport
## Down_3 Protein export
## Down_4 Non-homologous end-joining
## Down_5 mRNA surveillance pathway
## Down_6 Ubiquitin mediated proteolysis
## Down_7 Prolactin signaling pathway
## Down_8 Oocyte meiosis
## Down_9 Hepatitis B
## Down_10 Protein processing in endoplasmic reticulum
## Cl118_54 (54/54)
## Up_1 Ribosome
## Up_2 mRNA surveillance pathway
## Up_3 Circadian rhythm
## Up_4 Spliceosome
## Up_5 RNA transport
## Up_6 Necroptosis
## Up_7 Ubiquitin mediated proteolysis
## Up_8 Basal transcription factors
## Up_9 SNARE interactions in vesicular transport
## Up_10 Natural killer cell mediated cytotoxicity
## Down_1 Phenylalanine metabolism
## Down_2 Staphylococcus aureus infection
## Down_3 African trypanosomiasis
## Down_4 Autoimmune thyroid disease
## Down_5 Malaria
## Down_6 Taste transduction
## Down_7 Tyrosine metabolism
## Down_8 Human immunodeficiency virus 1 infection
## Down_9 Epstein-Barr virus infection
## Down_10 C-type lectin receptor signaling pathway