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source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/SingleFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/SingleFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/SingleFunctionTaxaContributionPlots.R')
devtools::create("FishTacoPlot")
getwd()
cd ..
setwd("/Volumes/ohadm/METAFIT/Rcode")
getwd()
devtools::create("FishTacoPlot")
devtools::document()
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/SingleFunctionTaxaContributionPlots.R')
setwd("/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/")
getwd()
devtools::document()
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
devtools::document()
devtools::document()
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
devtools::document()
library(FishTacoPlot)
devtools::document()
library(FishTacoPlot)
library(FishTacoPlot)
devtools::document()
source('/Volumes/ohadm/METAFIT/Rcode/FishTacoPlot/R/SingleFunctionTaxaContributionPlots.R')
library(FishTacoPlot)
devtools::document()
source('/Volumes/ohadm/BorensteinLab/PROJECTS/FISHTACO_OM/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
source('/Volumes/ohadm/BorensteinLab/PROJECTS/FISHTACO_OM/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.05)
install.packages("/Users/ManorLab/Desktop/fishtaco-plot-1.0.0", repos = NULL, type="source"); require(FishTacoPlot); require(ggplot2); require(scales)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.05)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.05, color_small_cont_by_phyla = FALSE)
source('/Volumes/ohadm/BorensteinLab/PROJECTS/FISHTACO_OM/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.05)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.025)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.02)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.025, min_contribution = 0)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.025, min_contribution = 0, show_only_diff_abun_taxa = TRUE)
MultiFunctionTaxaContributionPlots(input_dir="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples", input_prefix="HMP_fishtaco", input_taxa_taxonomy="/Users/ManorLab/Desktop/fishtaco-plot-1.0.0/examples/HMP_TAXONOMY.tab", sort_by="list", plot_type="bars",input_function_filter_list=c("ko00020", "ko00540","ko02040"), add_predicted_da_markers=TRUE, add_original_da_markers=TRUE, min_cont_as_separate = 0.025)
source('/Volumes/ohadm/BorensteinLab/PROJECTS/FISHTACO_OM/METAFIT/Rcode/FishTacoPlot/R/MultiFunctionTaxaContributionPlots.R')
devtools::document()