Hi, I have been trying to graph my CAFE5 results analysis from the file base_clade_results.txt. I have tried the tree annotation with the use specified annotation and using the .txt file with increases and decreases at each taxon ID as a data frame but I keep getting the error must request at least one colour from the hue palette (even when i try it with the example). I have also tried to do this through the advanced tree annotation section but with no luck! So I was wondering if there was a way to plot my cafe results using ggtree. The results look like this
Taxon_ID Increase Decrease
<75> 61 237
<51> 14 166
<29> 40 114
<58> 15 264
<66> 127 218
<64> 116 469
<69> 62 632
Eublepharismacularius<50> 571 724
<68> 19 519
Gopherusevgoodei<59> 1597 2004
<56> 298 242
<73> 35 375
Ceratotheriumsimum<16> 334 465
and I was attempting to produce a plot similar to this:
My tree also looks like this (((((((Pogonavitticeps:144.0,Varanuskomodoensis:144.0):29.0,Pseudonajatextilis:173.0):17.0,Eublepharismacularius:190.0):53.0,Sphenodonpunctatus:243.0):52.0,(Gopherusevgoodei:275.0,(Alligatormississippiensis:240.0,(((((((Taeniopygiaguttata:64.0,Aquilachrysaetos:64.0):1.0,Nipponianippon:65.0):1.0,Rissatridactyla:66.0):1.0,(Apusapus:66.0,cuculuscanorus:66.0):1.0):1.0,Columbalivia:68.0):22.0,Numidameleagris:90.0):12.0,Dromaiusnovaehollandiae:102.0):138.0):35.0):20.0):25.0,(Ornithorhynchusanatinus:200.0,(Sarcophilusharrisi:160.0,((Choloepusdidactylus:65.3,Elephasmaximum:65.3):29.7,((Desmodusrotundus:81.0,((Balaenopteramusculus:55.0,Susscrofa:55.0):5.0,Ceratotheriumsimum:60.0):21.0):5.0,(Nannosplalaxgalili:80.7,(Tupaiachinensis:74.0,Gorillagorilla:74.0):6.7):5.3):9.0):65.0):40.0):120.0):30.0,((Rhinatremabivittatum:135.0,(Geotrypetesseraphini:55.0,Microcaeciliauniclour:55.0):80.0):202.03,(Pleurodeleswatl:315.0,(Bombinabombina:190.0,((XenopusLaevis:45.0,XenopusTropicalis:45.0):135.0,((Speabombifrons:125.0,Leptobrachiumleishanense:125.0):45.0,(Bufobufo:130.0,(Nanoranaparkeri:60.0,Ranatemporaria:60.0):70.0):40.0):10.0):10.0):125.0):22.03):12.97);
Would it still be possible to keep the ultrametric tree and replace the labels with increase/decrease numbers for each branch?
Thank you!
Hi, I have been trying to graph my CAFE5 results analysis from the file base_clade_results.txt. I have tried the tree annotation with the use specified annotation and using the .txt file with increases and decreases at each taxon ID as a data frame but I keep getting the error must request at least one colour from the hue palette (even when i try it with the example). I have also tried to do this through the advanced tree annotation section but with no luck! So I was wondering if there was a way to plot my cafe results using ggtree. The results look like this
Taxon_ID Increase Decrease
<75> 61 237 <51> 14 166 <29> 40 114 <58> 15 264 <66> 127 218 <64> 116 469 <69> 62 632 Eublepharismacularius<50> 571 724 <68> 19 519 Gopherusevgoodei<59> 1597 2004 <56> 298 242 <73> 35 375 Ceratotheriumsimum<16> 334 465 and I was attempting to produce a plot similar to this: