lineagePath finds the lineages of a phylogenetic tree
providing the corresponding sequence alignment. This is done by finding
'major SNPs' which usually accumulate along the evolutionary pathways.
sneakPeek is intended to plot 'similarity' (actually the
least percentage of 'major SNP') as a threshold against number of output
lineagePath. This plot is intended to give user a rough view about how many
lineages they could expect from the 'similarity' threshold in the function
lineagePath. The number of lineagePath is preferably not be
too many or too few. The result excludes where the number of lineagePath is
greater than number of tips divided by 20 or user-defined maxPath. The zero
lineagePath result will also be excluded.
When used on the return of sneakPeek, a
lineagePath with the closest similarity will be retrieved
from the returned value.
similarity has no effect when using on
paraFixSites object
lineagePath(tree, similarity, ...)
# S3 method for phylo
lineagePath(
tree,
similarity = NULL,
alignment = NULL,
seqType = c("AA", "DNA", "RNA"),
reference = NULL,
gapChar = "-",
minSkipSize = NULL,
...
)
# S3 method for treedata
lineagePath(tree, ...)
# S3 method for phyMSAmatched
lineagePath(
tree,
similarity = NULL,
simMatrix = NULL,
forbidTrivial = TRUE,
...
)
sneakPeek(tree, step = 9, maxPath = NULL, minPath = 0, makePlot = TRUE)
# S3 method for sneakPeekedPaths
lineagePath(tree, similarity, ...)
# S3 method for paraFixSites
lineagePath(tree, similarity = NULL, ...)Arguments
- tree
The return from
addMSAorsneakPeekfunction.- similarity
The parameter for identifying phylogenetic pathway using SNP. If provided as fraction between 0 and 1, then the minimum number of SNP will be total tips times
Nmin. If provided as integer greater than 1, the minimum number will beNmin.- ...
Other arguments.
- alignment
An
alignmentobject. This commonly can be from sequence parsing function in theseqinrpackage. Sequence names in the alignment should include alltip.labelin the tree- seqType
The type of the sequence in the alignment file. The default is "AA" for amino acid. The other options are "DNA" and "RNA".
- reference
Name of reference for site numbering. The name has to be one of the sequences' name. The default uses the intrinsic alignment numbering
- gapChar
The character to indicate gap. The numbering will skip the
gapCharfor the reference sequence.- minSkipSize
The minimum number of tips to have gap or ambiguous amino acid/nucleotide for a site to be ignored in other analysis. This will not affect the numbering. The default is 0.8.
- simMatrix
Deprecated and will not have effect.
- forbidTrivial
Does not allow trivial trimming.
- step
the 'similarity' window for calculating and plotting. To better see the impact of threshold on path number. The default is 10.
- maxPath
maximum number of path to return show in the plot. The number of path in the raw tree can be far greater than trimmed tree. To better see the impact of threshold on path number. This is preferably specified. The default is one 20th of tree tip number.
- minPath
minimum number of path to return show in the plot. To better see the impact of threshold on path number. The default is 1.
- makePlot
Whether make a plot when return.
Value
Lineage path represent by node number.
sneakPeek return the similarity threhold against number of
lineagePath. There will be a simple dot plot between threshold and path
number if makePlot is TRUE.
Examples
data('zikv_tree')
data('zikv_align')
tree <- addMSA(zikv_tree, alignment = zikv_align)
lineagePath(tree)
#> This is a 'lineagePath' object.
#>
#> 7 lineage paths using 8 as "major SNP" threshold
sneakPeek(tree, step = 3)
#> similarity pathNum
#> 1 0.005524862 46
#> 2 0.008287293 26
#> 3 0.011049724 15
#> 4 0.013812155 11
#> 5 0.016574586 9
#> 6 0.019337017 8
#> 7 0.022099448 7
#> 8 0.024861878 7
#> 9 0.027624309 6
#> 10 0.030386740 5
#> 11 0.033149171 5
#> 12 0.035911602 5
#> 13 0.038674033 5
#> 14 0.041436464 5
#> 15 0.044198895 4
#> 16 0.046961326 4
#> 17 0.049723757 4
#> 18 0.052486188 4
#> 19 0.055248619 4
#> 20 0.058011050 4
#> 21 0.060773481 4
#> 22 0.063535912 4
#> 23 0.066298343 4
#> 24 0.069060773 4
#> 25 0.071823204 4
#> 26 0.074585635 4
#> 27 0.077348066 4
#> 28 0.080110497 4
#> 29 0.082872928 4
#> 30 0.085635359 4
#> 31 0.088397790 4
#> 32 0.091160221 4
#> 33 0.093922652 4
#> 34 0.096685083 4
#> 35 0.099447514 4
#> 36 0.102209945 4
#> 37 0.104972376 4
#> 38 0.107734807 4
#> 39 0.110497238 4
#> 40 0.113259669 4
#> 41 0.116022099 4
#> 42 0.118784530 4
#> 43 0.121546961 4
#> 44 0.124309392 4
#> 45 0.127071823 4
#> 46 0.129834254 4
#> 47 0.132596685 4
#> 48 0.135359116 4
#> 49 0.138121547 4
#> 50 0.140883978 3
#> 51 0.143646409 3
#> 52 0.146408840 3
#> 53 0.149171271 3
#> 54 0.151933702 3
#> 55 0.154696133 3
#> 56 0.157458564 3
#> 57 0.160220994 2
#> 58 0.162983425 2
#> 59 0.165745856 2
#> 60 0.168508287 2
#> 61 0.171270718 2
#> 62 0.174033149 2
#> 63 0.176795580 2
#> 64 0.179558011 2
#> 65 0.182320442 2
#> 66 0.185082873 2
#> 67 0.187845304 2
#> 68 0.190607735 2
#> 69 0.193370166 2
#> 70 0.196132597 2
#> 71 0.198895028 2
#> 72 0.201657459 2
#> 73 0.204419890 2
#> 74 0.207182320 2
#> 75 0.209944751 2
#> 76 0.212707182 2
#> 77 0.215469613 2
#> 78 0.218232044 2
#> 79 0.220994475 2
#> 80 0.223756906 2
#> 81 0.226519337 2
#> 82 0.229281768 2
#> 83 0.232044199 2
#> 84 0.234806630 2
#> 85 0.237569061 2
#> 86 0.240331492 2
#> 87 0.243093923 2
#> 88 0.245856354 2
#> 89 0.248618785 2
#> 90 0.251381215 2
#> 91 0.254143646 2
#> 92 0.256906077 2
#> 93 0.259668508 2
#> 94 0.262430939 2
#> 95 0.265193370 2
#> 96 0.267955801 2
#> 97 0.270718232 1
#> 98 0.273480663 1
#> 99 0.276243094 1
#> 100 0.279005525 1
#> 101 0.281767956 1
#> 102 0.284530387 1
#> 103 0.287292818 1
#> 104 0.290055249 1
#> 105 0.292817680 1
#> 106 0.295580110 1
#> 107 0.298342541 1
#> 108 0.301104972 1
#> 109 0.303867403 1
#> 110 0.306629834 1
#> 111 0.309392265 1
#> 112 0.312154696 1
#> 113 0.314917127 1
#> 114 0.317679558 1
#> 115 0.320441989 1
#> 116 0.323204420 1
#> 117 0.325966851 1
#> 118 0.328729282 1
#> 119 0.331491713 1
#> 120 0.334254144 1
#> 121 0.337016575 1
#> 122 0.339779006 1
#> 123 0.342541436 1
#> 124 0.345303867 1
#> 125 0.348066298 1
#> 126 0.350828729 1
#> 127 0.353591160 1
#> 128 0.356353591 1
#> 129 0.359116022 1
#> 130 0.361878453 1
#> 131 0.364640884 1
#> 132 0.367403315 1
#> 133 0.370165746 1
#> 134 0.372928177 1
#> 135 0.375690608 1
#> 136 0.378453039 1
#> 137 0.381215470 1
#> 138 0.383977901 1
#> 139 0.386740331 1
#> 140 0.389502762 1
#> 141 0.392265193 1
#> 142 0.395027624 1
#> 143 0.397790055 1
#> 144 0.400552486 1
#> 145 0.403314917 1
#> 146 0.406077348 1
#> 147 0.408839779 1
#> 148 0.411602210 1
#> 149 0.414364641 1
#> 150 0.417127072 1
#> 151 0.419889503 1
#> 152 0.422651934 1
#> 153 0.425414365 1
#> 154 0.428176796 1
#> 155 0.430939227 1
#> 156 0.433701657 1
#> 157 0.436464088 1
#> 158 0.439226519 1
#> 159 0.441988950 1
#> 160 0.444751381 1
#> 161 0.447513812 1
#> 162 0.450276243 1
#> 163 0.453038674 1
#> 164 0.455801105 1
#> 165 0.458563536 1
#> 166 0.461325967 1
#> 167 0.464088398 1
#> 168 0.466850829 1
#> 169 0.469613260 1
#> 170 0.472375691 1
#> 171 0.475138122 1
#> 172 0.477900552 1
#> 173 0.480662983 1
#> 174 0.483425414 1
#> 175 0.486187845 1
#> 176 0.488950276 1
#> 177 0.491712707 1
#> 178 0.494475138 1
#> 179 0.497237569 1
#> 180 0.500000000 1
x <- sneakPeek(tree, step = 3)
lineagePath(x, similarity = 0.05)
#> This is a 'lineagePath' object.
#>
#> 4 lineage paths using 19 as "major SNP" threshold