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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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phylotree_analyze defaults to downsampled #72

Closed evandiego83 closed 7 months ago

evandiego83 commented 1 year ago

Hello again developers,

I am having an issue where I have not selected dowsampling for my analysis and yet the trees I get back from running the 2nd step analyze_trees shows that the trees are darkened out on the pdf and those tips are labelled count_o_X_dowsampled.

Is this the new default behavior or is there a way to turn this off (Even though I am not selecting for it!)

Thank you Evan

evandiego83 commented 1 year ago

Even using the example outputs I get the same typeof behavior 

Random number seed is 672525553 
Warning in phyloscanner.analyse.trees(tree.directory, tree.file.regex, reconstruction.mode,  :
  Dual blacklisting requires parsimony blacklisting. Turning dual blacklisting off.
Warning in classify(ptree, allow.mt, n.mt, p.mt, zero.length.adjustment,  :
  n.mt and p.mt were all specified, and only p.mt was used.

Warning: There was 1 warning in `transmute()`.
ℹ In argument: `across(.fns = function(x) x/ptree$normalisation.constant)`.
Caused by warning:
! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0.
ℹ Please supply `.cols` instead.
mdhall272 commented 1 year ago

What is the exact phyloscanner command you used?

evandiego83 commented 1 year ago

./phyloscanner_analyse_trees.R ExampleOutputData_FromMakeTrees/RAxMLfiles/RAxML_bestTree.InWindow_ TEST s,20 --multifurcationThreshold g

mdhall272 commented 1 year ago

I can't replicate the problem. No downsampling is done and no messages regarding blacklisting appear when I run that command:

Warning: No outgroup name provided. Trees are assumed to be correctly rooted.
Random number seed is 948469481
Initialising...
Checking for window coordinates in tree identifiers...found
Reading trees...
Checking for read counts in tip names...found
Warning in initialise.phyloscanner(tree.file.directory, tree.file.regex,  :
  Attempting to guess a branch length threshold for multifurcations from the tree. Please visually examine the tree or trees for multifurcations before using the results of this analysis.
Preparing trees...
Gathering host IDs...
***The full list of host IDs that will be used in this analysis follows. If this is not what you intended, check your --tipRegex***
contaminator
contaminee
donor
dual
recipient
single
Performing the parsimony reconstruction...
Finding host MRCAs for summary statistics...
Classifying pairwise host relationships...
Writing annotated trees in .pdf format...
Calculating per-host summary statistics...
Writing summary statistics to file TEST_patStats.csv...
Graphing summary statistics to file TEST_patStats.pdf...
Writing transmission summary to file TEST_hostRelationshipSummary.csv...
Drawing simplified summary diagram to file TEST_simplifiedRelationshipGraph.pdf...
Finished.