pCorShrink on ecostructure data

Packages

library(CorShrink)
library(ecostructure)
library(corpcor)
library(corrplot)
library(network)
library(statnet)
library(scales)
library(Biobase)
library(limma)

Data

data("himalayan_birds")
birds <- exprs(himalayan_birds)
log_cpm_birds <- t(limma::voom(birds)$E)
ymat = scale(log_cpm_birds, scale = TRUE, center = TRUE)

pcor2 <- pCorShrinkData(ymat, reg_type = "glmnet", glmnet_alpha = 0.8)
col2 <- c("blue", "white", "red")
corrplot(pcor2, diag = FALSE, col = colorRampPalette(col2)(200), tl.pos = "td", 
         tl.col = "black", tl.cex = 0.8, rect.col = "white", 
         na.label.col = "white", method = "color", type = "upper")

colnames(pcor2) <- c(rownames(birds))
rownames(pcor2) <- colnames(pcor2)

tmp <- pcor2[lower.tri((pcor2))]
idx1 <- order(tmp, decreasing = TRUE)[1:25]
idx2 <- order(tmp, decreasing = FALSE)[1:25]

tmp[idx1]

##  [1] 0.9888860 0.9886311 0.7658025 0.7599949 0.7118505 0.7005307 0.6928543
##  [8] 0.6826790 0.6572590 0.6156191 0.6129314 0.6073927 0.6000300 0.5954638
## [15] 0.5888494 0.5858971 0.5854348 0.5672162 0.5496850 0.5462277 0.5426408
## [22] 0.5354098 0.5279475 0.5258894 0.5122830

tmp[idx2]

##  [1] -0.9603030 -0.9382375 -0.8984661 -0.8693361 -0.8640522 -0.8608445
##  [7] -0.8431629 -0.8328228 -0.8151713 -0.8010064 -0.7987693 -0.7929924
## [13] -0.7917160 -0.7894634 -0.7883849 -0.7861321 -0.7831861 -0.7759119
## [19] -0.7679360 -0.7656134 -0.7620676 -0.7608243 -0.7561347 -0.7529231
## [25] -0.7513484

bird_pairs <- combn(colnames(pcor2),2)

Positively associated Birds

t(bird_pairs[,idx1])

##       [,1]                        [,2]                       
##  [1,] "Paradoxornis_ruficeps"     "Paradoxornis_gularis"     
##  [2,] "Monticola_cinclorhynchus"  "Saxicola_ferreus"         
##  [3,] "Leiothrix_argentauris"     "Paradoxornis_ruficeps"    
##  [4,] "Hypopicus_hyperythrus"     "Aceros_undulatus"         
##  [5,] "Zoothera_mollissima"       "Cochoa_purpurea"          
##  [6,] "Harpactes_erythrocephalus" "Harpactes_wardi"          
##  [7,] "Paradoxornis_nipalensis"   "Conostoma_oemodium"       
##  [8,] "Emberiza_fucata"           "Pyrrhula_aurantiaca"      
##  [9,] "Coracina_macei"            "Dicrurus_remifer"         
## [10,] "Paradoxornis_gularis"      "Coracina_macei"           
## [11,] "Psarisomus_dalhousiae"     "Pitta_brachyura"          
## [12,] "Picus_xanthopygaeus"       "Cettia_pallidipes"        
## [13,] "Pteruthius_flaviscapis"    "Pteruthius_melanotis"     
## [14,] "Mycerobas_affinis"         "Mycerobas_carnipes"       
## [15,] "Merops_orientalis"         "Megalaima_haemacephala"   
## [16,] "Pteruthius_xanthochlorus"  "Oriolus_kundoo"           
## [17,] "Oriolus_xanthornus"        "Oriolus_traillii"         
## [18,] "Carpodacus_rubescens"      "Pyrrhoplectes_epauletta"  
## [19,] "Parus_ater"                "Parus_dichrous"           
## [20,] "Phaenicophaeus_tristis"    "Ceyx_erithaca"            
## [21,] "Pericrocotus_roseus"       "Abroscopus_albogularis"   
## [22,] "Luscinia_pectoralis"       "Hodgsonius_phaenicuroides"
## [23,] "Cuculus_saturatus"         "Cuculus_canorus"          
## [24,] "Psittacula_cyanocephala"   "Abroscopus_albogularis"   
## [25,] "Seicercus_burkii"          "Seicercus_poliogenys"

Negatively associated Birds

t(bird_pairs[,idx2])

##       [,1]                      [,2]                     
##  [1,] "Sturnia_malabarica"      "Psittacula_cyanocephala"
##  [2,] "Spelaeornis_formosus"    "Abroscopus_albogularis" 
##  [3,] "Leiothrix_lutea"         "Cettia_pallidipes"      
##  [4,] "Napothera_epilepidota"   "Yuhina_bakeri"          
##  [5,] "Heterophasia_annectans"  "Pericrocotus_solaris"   
##  [6,] "Muscicapella_hodgsoni"   "Spelaeornis_caudatus"   
##  [7,] "Paradoxornis_fulvifrons" "Pyrrhoplectes_epauletta"
##  [8,] "Aceros_nipalensis"       "Napothera_epilepidota"  
##  [9,] "Brachypteryx_leucophrys" "Heterophasia_annectans" 
## [10,] "Pericrocotus_roseus"     "Psittacula_cyanocephala"
## [11,] "Brachypteryx_hyperythra" "Actinodura_waldeni"     
## [12,] "Actinodura_nipalensis"   "Picus_xanthopygaeus"    
## [13,] "Phyllergates_cucullatus" "Heterophasia_annectans" 
## [14,] "Ocyceros_birostris"      "Acridotheres_tristis"   
## [15,] "Niltava_grandis"         "Pteruthius_flaviscapis" 
## [16,] "Prinia_socialis"         "Spelaeornis_caudatus"   
## [17,] "Heterophasia_annectans"  "Heterophasia_picaoides" 
## [18,] "Spelaeornis_caudatus"    "Dicaeum_ignipectus"     
## [19,] "Leiothrix_argentauris"   "Paradoxornis_gularis"   
## [20,] "Fulvetta_vinipectus"     "Carpodacus_rubescens"   
## [21,] "Pycnonotus_cafer"        "Cinnyris_asiaticus"     
## [22,] "Sitta_formosa"           "Heterophasia_annectans" 
## [23,] "Phoenicurus_frontalis"   "Spelaeornis_caudatus"   
## [24,] "Cyornis_unicolor"        "Phylloscopus_cantator"  
## [25,] "Liocichla_phoenicea"     "Yuhina_bakeri"