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nclark-lab / RERconverge

Analysis of convergence between organismal traits and DNA/protein sequences
GNU General Public License v3.0
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A large number of Duplicate columns and NA columns after running getAllResiduals #95

Closed huziouziou closed 5 months ago

huziouziou commented 5 months ago

I use the estimatePhangornTreeAll() function to get the tree file for all my sequences. Attached the trees I am using here. all_cne_Phangorn_tree.txt Most of trees have all 17 species, and a few are missing 1-2 species. Then I read my tree with readTrees() and compute RER with getAllResiduals(). I get the following waning message:

cutoff is set to 2e-08 i= 1 i= 2 i= 12 i= 32 i= 89 i= 365 i= 387 Naming rows and columns of RER matrix Warning message: In regularize.values(x, y, ties, missing(ties), na.rm = na.rm) : collapsing to unique 'x' values

I ignored the warning and continued to calculate

ice.fish.tree <- foreground2Tree(foreground = ice_fishes,
                                  treesObj = all_fishes_tree,
                                  clade = "all")
pathvec <- tree2Paths(ice.fish.tree,all_fishes_tree)
res <- correlateWithBinaryPhenotype(all_fishesRER,pathvec)

I got results, but there are some issues confusing me.

1.When I wanted to plotRers(), I failed. Then I found that there are a large number of duplicate columns and NA clolumns in my RER matrix

> colnames(all_fishesRER)
  [1] "Danio_rerio"                   "Chionodraco_myersi"           
  [3] "Chionodraco_myersi"            "Chionodraco_myersi"           
  [5] "Chionodraco_myersi"            "Chionodraco_myersi"           
  [7] "Chionodraco_myersi"            "Chionodraco_myersi"           
  [9] "Chionodraco_myersi"            "Chionodraco_myersi"           
 [11] "Chionodraco_myersi"            "Chionodraco_myersi"           
 [13] "Chionodraco_myersi"            "Chionodraco_myersi"           
 [15] "Chionodraco_hamatus"           "Chionodraco_hamatus"          
 [17] "Chionodraco_hamatus"           "Chionodraco_hamatus"          
 [19] "Chionodraco_hamatus"           "Chionodraco_hamatus"          
 [21] "Chionodraco_hamatus"           "Chionodraco_hamatus"          
 [23] "Chionodraco_hamatus"           "Chionodraco_hamatus"          
 [25] "Chionodraco_hamatus"           "Chionodraco_hamatus"          
 [27] "Chionodraco_hamatus"           "Chaenocephalus_aceratus"      
 [29] "Chaenocephalus_aceratus"       "Chaenocephalus_aceratus"      
 [31] "Chaenocephalus_aceratus"       "Chaenocephalus_aceratus"      
 [33] "Chaenocephalus_aceratus"       "Chaenocephalus_aceratus"      
 [35] "Chaenocephalus_aceratus"       "Chaenocephalus_aceratus"      
 [37] "Chaenocephalus_aceratus"       "Chaenocephalus_aceratus"      
 [39] "Chaenocephalus_aceratus"       "Pseudochaenichthys_georgianus"
 [41] "Pseudochaenichthys_georgianus" "Pseudochaenichthys_georgianus"
 [43] "Pseudochaenichthys_georgianus" "Pseudochaenichthys_georgianus"
 [45] "Pseudochaenichthys_georgianus" "Pseudochaenichthys_georgianus"
 [47] "Pseudochaenichthys_georgianus" "Pseudochaenichthys_georgianus"
 [49] "Pseudochaenichthys_georgianus" "Pseudochaenichthys_georgianus"
 [51] "Gymnodraco_acuticeps"          "Gymnodraco_acuticeps"         
 [53] "Gymnodraco_acuticeps"          "Gymnodraco_acuticeps"         
 [55] "Gymnodraco_acuticeps"          "Gymnodraco_acuticeps"         
 [57] "Gymnodraco_acuticeps"          "Gymnodraco_acuticeps"         
 [59] "Gymnodraco_acuticeps"          "Gymnodraco_acuticeps"         
 [61] "Harpagifer_antarcticus"        "Harpagifer_antarcticus"       
 [63] "Harpagifer_antarcticus"        "Harpagifer_antarcticus"       
 [65] "Harpagifer_antarcticus"        "Harpagifer_antarcticus"       
 [67] "Harpagifer_antarcticus"        "Harpagifer_antarcticus"       
 [69] "Harpagifer_antarcticus"        "Trematomus_bernacchii"        
 [71] "Trematomus_bernacchii"         "Trematomus_bernacchii"        
 [73] "Trematomus_bernacchii"         "Trematomus_bernacchii"        
 [75] "Trematomus_bernacchii"         "Trematomus_bernacchii"        
 [77] "Trematomus_bernacchii"         "Dissostichus_mawsoni"         
 [79] "Dissostichus_mawsoni"          "Dissostichus_mawsoni"         
 [81] "Dissostichus_mawsoni"          "Dissostichus_mawsoni"         
 [83] "Dissostichus_mawsoni"          "Dissostichus_mawsoni"         
 [85] "Eleginops_maclovinus"          "Eleginops_maclovinus"         
 [87] "Eleginops_maclovinus"          "Eleginops_maclovinus"         
 [89] "Eleginops_maclovinus"          "Eleginops_maclovinus"         
 [91] "Cottoperca_gobio"              "Cottoperca_gobio"             
 [93] "Cottoperca_gobio"              "Cottoperca_gobio"             
 [95] "Cottoperca_gobio"              "Sebastes_aleutianus"          
 [97] "Sebastes_aleutianus"           "Sebastes_aleutianus"          
 [99] "Sebastes_aleutianus"           "Sebastes_aleutianus"          
[101] "Gasterosteus_aculeatus"        "Gasterosteus_aculeatus"       
[103] "Gasterosteus_aculeatus"        "Gasterosteus_aculeatus"       
[105] "Gasterosteus_aculeatus"        "Perca_flavescens"             
[107] "Perca_flavescens"              "Perca_flavescens"             
[109] "Oryzias_latipes"               "Oryzias_latipes"              
[111] "Oryzias_latipes"               "Mastacembelus_armatus"        
[113] "Mastacembelus_armatus"         "Mastacembelus_armatus"        
[115] "Thamnaconus_septentrionalis"   NA                             
[117] NA                              NA                             
[119] NA                              NA                             
[121] NA                              NA                             
[123] NA                              NA                             
[125] NA                              NA                             
[127] NA                              NA                             
[129] NA                              NA                             
[131] NA                              NA                             
[133] NA                              NA                             
[135] NA                              NA                             
[137] NA                              NA                             
[139] NA                              NA                             
[141] NA                              NA                             
[143] NA                              NA                             
[145] NA                              NA                             
[147] NA                              NA                             
[149] NA                              NA                             
[151] NA                              NA                             
[153] NA                              NA                             
[155] NA                              NA                             
[157] NA                              NA                             
[159] NA                              NA                             
[161] NA                              NA                             
[163] NA                              NA                             
[165] NA                              NA                             
[167] NA                              NA                             
[169] NA                              NA                             
[171] NA                              NA                             
[173] NA                              NA                             
[175] NA                              NA                             
[177] NA                              NA                             
[179] NA                              NA                             
[181] NA                              NA                             
[183] NA                              NA                             
[185] NA                              NA                             
[187] NA                              NA                             
[189] NA                              NA                             
[191] NA                              NA                             
[193] NA                              NA                             
[195] NA                              NA                             
[197] NA                              NA                             
[199] NA
  1. The second problem is if I want to use foreground2TreeClades() to generates a binary phenotype tree by setting sisters species, I will get noting. No error, No results, just stuck. I don't know why.

I don't know if my results are correct and valid. Now it makes me so confusing. Thanks!!!

huziouziou commented 5 months ago

Everything is OK, but I made a stupid mistake and entered the wrong parameters when plotting.