Rainbow Tree Explanation
The input for rainbow tree is a tree in Newick format. To generate a Newick tree file from aligned sequences try:
The Sample Input example depicts the HIV-1 M-group reference phylogeny, with the sequences labeled as obtained from our sequence database. For example:
A1.AU.03.PS1044_Day0.DQ676872
is clade A1, from Australia (AU), sampled in 2003 (03), named PS1044_Day0, with accession number DQ676872.
For these 5 sequences from the Sample Input:
A1.AU.03.PS1044_Day0.DQ676872 A1.UG.92.92UG037.AB253429 B.TH.90.BK132.AY173951 F1.BE.93.VI850.AF077336 F2.CM.02.02CM_0016BBY.AY371158
If the first character was selected for the color key, then A, B, and F would each be assigned a color.
If the first field delineated by a period was selected, then A1, B, and F1 and F2 would each be assigned a color.
If the second field delineated by periods was selected, the five country codes (AU, UG, TH, BE and CM) would each be assigned a color.
Rainbow tree can create a tree of up to 20 colors.
| ● | Red | ● | Orange | ● | Yellow | ● | Yellow green | ● | Green |
| ● | Blue | ● | Royal blue | ● | Dark orchid | ● | Deep pink | ● | Hot pink |
| ● | Light pink | ● | Brown | ● | Khaki | ● | Lemon chiffon | ● | Teal |
| ● | Medium turquoise | ● | Sky blue | ● | Medium purple | ● | Medium slate blue | ● | Grey |
With the default color assignment, the most frequent category will be red, the next most frequent orange, etc. For trees with more than 20 categories, the last color (grey) is re-used for all additional categories, and this is noted in the key. The user may specify their own color choice for each category. Colors are limited to 20, as it becomes difficult to distinguish more than 20 colors in a tree.
If unchecked, tree will be unrooted. If checked, you will have the option of choosing an outgroup to root the tree.
Below is an example of grouped sequence names. Groups are specified as lists of sequence names. Each sequence must be on a separate line, and groups are separated by an empty line. The first item ending in ':' in a group will be taken as the group name, but this line is optional. If group names are omitted, the names Group-1, Group-2, etc., will be generated for reporting. Sequences that are not present in any group will be named 'Others' and colored gray. This is useful for highlighting some groups of sequences out of a target set.
The following can be pasted in with the Sample Input for testing the Grouped Sequence Names option:
Group-A: A1.AU.03.PS1044_Day0.DQ676872 A1.RW.92.92RW008.AB253421 A1.UG.92.92UG037.AB253429 A2.CD.97.97CDKTB48.AF286238 A2.CM.01.01CM_1445MV.GU201516 A2.CY.94.94CY017_41.AF286237 B.FR.83.HXB2_LAI_IIIB_BRU.K03455 B.TH.90.BK132.AY173951 B.US.98.1058_11.AY331295 B.NL.00.671_00T36.AY423387 Group-B: D.CD.83.ELI.K03454 D.CM.01.01CM_4412HAL.AY371157 D.TZ.01.A280.AY253311 D.UG.94.94UG114.U88824 F1.BE.93.VI850.AF077336 F1.FI.93.FIN9363.AF075703 F1.BR.93.93BR020_1.AF005494 F1.FR.96.96FR_MP411.AJ249238
Symbols can be applied to branch tips instead of text.
At right, the number next to each symbol is used to specify that symbol.
Symbols can be assigned to groups of sequences. Groups are specified as lists of sequence names. Each sequence must be on a separate line, and groups are separated by an empty line. The first line in a group must contain 2 colon-separated values ending in ':' (e.g., 3:Male: ). These values will be taken as the symbol id and group name. Sequences that are not present in any group will be grouped as 'Unknown', and a bullet (smaller than symbol #16) will be assigned.
The following example can be pasted in with the Sample Input for testing the symbol tip option:
0:Male: A1.AU.03.PS1044_Day0.DQ676872 A1.UG.92.92UG037.AB253429 A2.CD.97.97CDKTB48.AF286238 A2.CY.94.94CY017_41.AF286237 B.FR.83.HXB2_LAI_IIIB_BRU.K03455 B.NL.00.671_00T36.AY423387 D.CD.83.ELI.K03454 D.TZ.01.A280.AY253311 F1.BE.93.VI850.AF077336 F1.FR.96.96FR_MP411.AJ249238 F2.CM.02.02CM_0016BBY.AY371158 K.CM.96.96CM_MP535.AJ249239 J.CD.97.J_97DC_KTB147.EF614151 1:Female: A1.RW.92.92RW008.AB253421 A2.CM.01.01CM_1445MV.GU201516 B.TH.90.BK132.AY173951 B.US.98.1058_11.AY331295 C.IN.95.95IN21068.AF067155 D.CM.01.01CM_4412HAL.AY371157 D.UG.94.94UG114.U88824 F1.FI.93.FIN9363.AF075703 F1.BR.93.93BR020_1.AF005494 G.NG.92.92NG083.U88826 H.BE.93.VI997.AF190128
If checked, this option will propagate leaf colors inward (toward the root of the tree) until a mismatch is encountered.
If checked, this option displays the node labels from your Newick file. Our sample input does not contain node labels.
Usage
rainbowtree ( treefile, tablefile, treetitle, label = 'seqname', label4ut = 'axial',
legend = 'vertical', legendpos = 'bottomleft', branchwidth = 1, outgroup )
Arguments
| treefile | the newick tree file name |
| tablefile | the 2- or 3-column table file name. Sequence name (1st column), integer index (1-20) to colors on palette (2nd), and category (3rd). The 3rd column can be omitted when legend='none' and label='seqname'/'none' |
| treetitle | the tree title |
| label | a character string specifying the type of tip labels: 'category', 'seqname' or 'none'(no tip label) |
| label4ut | a character string specifying the display of tip labels for unrooted trees: 'axial' or 'horizontal' |
| legend | a character string specifying the legend style: 'vertical', 'horizontal' or 'none'(no legend) |
| legendpos | a character string specifying the location of legend: 'bottomright', 'bottom', 'bottomleft', 'left', 'topleft', 'top', 'topright', 'right' or 'center' |
| branchwidth | a positive number specifying the width of the branches |
| outgroup | vector of numeric or character specifying the new outgroup |
| color.int.edges | whether to propagate leaf colors upward into a tree until a mismatch is encountered: 'TRUE' or 'FALSE' |
Examples
source('rainbowtree.r')
rainbowtree( treefile='mytree.tre', tablefile='mytable.txt')
rainbowtree( treefile='mytree.tre', tablefile='mytable.txt', label='category', legend='horizontal')
rainbowtree( treefile='mytree.tre', tablefile='mytable.txt', label='none', branchwidth=3)
rainbowtree( treefile='/tmp/mytree.tre', tablefile='mytable.txt', outgroup=c('seqname1', 'seqname2'))
rainbowtree( treefile='/tmp/mytree.tre', tablefile='mytable.txt', legendpos='bottomright', outgroup=2)
Output trees
Output tree files are created in the directory where input files are.
- InfileName.u.pdf - radial tree in pdf
- InfileName.u.png - radial tree in png
- InfileName.p.pdf - phenogram in pdf
- InfileName.p.png - phenogram in png
- InfileName.fan.pdf - fan tree in pdf
- InfileName.fan.png - fan tree in png
