Commit 70898fe0 authored by NAVRATIL VINCENT's avatar NAVRATIL VINCENT
Browse files

added root clades

parent d62426ea
......@@ -8,12 +8,18 @@ library(gridExtra)
library(DT)
library(ggplot2)
library(ggtree)
library(ape)
library(ggmsa)
library(tidyverse)
library(readr)
colnames_focus <- c("File","Name","Gene","Description","GeneSize","NbSpecies","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","FUBAR","FUBAR_NbSites","FUBAR_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
colnames_full <- c("File","Name","Gene","Description","GeneSize","NbSpecies","omegaM0Bpp","omegaM0codeml","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
colnames_full <- c("File","Name","Gene","Description","GeneSize","NbSpecies","omegaM0Bpp","omegaM0codeml","BUSTED","BUSTED_p-value","MEME_NbSites","MEME_PSS","BppM1M2","BppM1M2_p-value","BppM1M2_NbSites","BppM1M2_PSS","BppM7M8","BppM7M8_p-value","BppM7M8_NbSites","BppM7M8_PSS","codemlM1M2","codemlM1M2_p-value","codemlM1M2_NbSites","codemlM1M2_PSS","codemlM7M8","codemlM7M8_p-value","codemlM7M8_NbSites","codemlM7M8_PSS")
#define root_clades
root_clade_bats <- "meglyr|rhiSin|rhiFer|hipArm|hipRub|eidHel|rouAeg|pteAle|pteVam"
#root_clade_primates <- "eulRuf|eulCol|eulFul|eulSan|eulAlb|eulMon|eulMac|eulCor|eulRub|hapOcc|hapGri|lemCat|varVar|lepSep|lepAnk|lepDor|lepRuf|lepJam|micMur|mirZaz|cheMed|proVer|proTat|proDia|proEdw|avaLan|dauMad|nycBen|nycCou|nycPyg|lorTar|arcCal|perPot|galSen|galMoh|otoGar|otoCra|galTho|galVar|cynVol|tupGli|tupMin"
root_clade_primates <- "nycBen|nycCou|nycPyg|lorTar|arcCal|perPot|galSen|galMoh|otoGar|otoCra|galTho|galVar|cynVol|tupGli|tupMin"
root_clades <- paste(root_clade_bats,root_clade_primates,sep="|")
\ No newline at end of file
......@@ -265,8 +265,9 @@ shinyServer(
phylopic_id="18bfd2fc-f184-4c3a-b511-796aafcc70f6"
}
rooted_tree <- root(tree,tree$tip.label %>% str_detect(root_clades) %>% which(),r=TRUE)
p <- ggtree(tree,size=1) + geom_tiplab(size=5)
p <- ggtree(rooted_tree,size=1) + geom_tiplab(size=5)
p_msa_window <- dginn_msaplot(p, paste(file_url,".fasta",sep=""), offset=1, width=5, window=c(120, 200))
......@@ -347,8 +348,8 @@ shinyServer(
phylopic_id="18bfd2fc-f184-4c3a-b511-796aafcc70f6"
}
p <- ggtree(tree,size=1) + geom_tiplab(size=5)
rooted_tree <- root(tree,tree$tip.label %>% str_detect(root_clades) %>% which(),r=TRUE)
p <- ggtree(rooted_tree,size=1) + geom_tiplab(size=5)
p_msa_window <- dginn_msaplot(p, paste(file_url,".best.fas",sep=""), offset=1, width=5, window=c(120, 200))
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment