Open synbioplayer opened 1 year ago
install.packages("devtools") source('http://bioconductor.org/biocLite.R') biocLite('phyloseq') source("http://bioconductor.org/biocLite.R") if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.16") a yes biocLite("phyloseq") source("http://bioconductor.org/biocLite.R") source("https://raw.githubusercontent.com/joey711/phyloseq/master/inst/scripts/installer.R", local = TRUE) yes install_github("beadyallen/MGnifyR") library("devtools") install_github("beadyallen/MGnifyR") library(MGnifyR)
mgnify_client(url = "https://www.ebi.ac.uk/metagenomics/api/v1", username = "Webin-63503", password = "qownstlrqkqhz!1", usecache = T, cache_dir = "/desktop/Mgnify_cache_location", warnings = F, use_memcache = F) mg <- mgnify_client(cache_dir = "/desktop/Mgnify_cache_location") mgnify_query(mg, qtype = "samples", maxhits=10, usecache = T) J <- mgnify_query(mg, qtype = "samples", biome_name = "insecta", maxhits=200, usecache = T) colnames(J) insect_samples = mgnify_query(mg, qtype="samples", biome_name = "insecta", experiment_type = "amplicon", maxhits=200, usecache = T) insect_samples_2 = mgnify_query(mg, qtype="samples", biome_name = "insect", experiment_type = "amplicon", maxhits=200, usecache = T) insect_samples_3 = mgnify_query(mg, qtype="samples", biome_name = "mosquito", experiment_type = "amplicon", maxhits=10, usecache = T) insect_samples_4 = mgnify_query(mg, qtype="samples", sample_name = "insecta", experiment_type = "amplicon", maxhits=10, usecache = T) insect_samples_mosquito = mgnify_query(mg, qtype="samples", environment_feature="Mosquito gut", experiment_type = "amplicon", maxhits=200, usecache = T) insect_samples_mosquito_2 = mgnify_query(mg, qtype="samples", environment_feature="Mosquito gut", maxhits=10, usecache = T) insect_samples_5 = mgnify_query(mg, qtype="runs", biome_name="insecta", maxhits=10, usecache = T) mgnify_query(mg, qtype="samples", biome_name = "insecta", experiment_type = "amplicon", maxhits=10, usecache = T) samp_acc <- insect_samples$accession samp_acc (an_acc <- mgnify_analyses_from_samples(mg, samp_acc)) metadata <- mgnify_get_analyses_metadata(mg, an_acc, usecache=T) head(metadata) colnames(metadata) amplicon_accessions <- metadata$analysis_accession[metadata$'analysis_experiment-type'=="amplicon"] ps <- mgnify_get_analyses_phyloseq(mg, amplicon_accessions) ps@otu_table ps@tax_table
samp_acc <- insect_studies$accession samp_acc (an_acc <- mgnify_analyses_from_samples(mg, samp_acc)) metadata <- mgnify_get_analyses_metadata(mg, an_acc, usecache=T) head(metadata) colnames(metadata) amplicon_accessions <- metadata$analysis_accession[metadata$'analysis_experiment-type'=="amplicon"] ps <- mgnify_get_analyses_phyloseq(mg, amplicon_accessions)
tax_table(ps) otu_table(ps) sample_data(ps) tax_table(ps)
psglom <- tax_glom(normed_ps, "Order") normed_ps <- transform_sample_counts(psglom, function(x) x/sum(x)) plot_bar(normed_ps, fill="Phylum")
ord <- ordinate(ps, "NMDS", "bray") plot_ordination(ps, ord) + geom_point(aes(color=as.numeric(sample_elevation)), size=8) + theme_bw()
mgnify_get_download_urls(client, accessions, accession_type) dl_df <- mgnify_get_download_urls(mg, acc_list, "analyses") head(dl_df)
table(metadata$'analysis_experiment-type' == "amplicon")
install.packages("devtools") source('http://bioconductor.org/biocLite.R') biocLite('phyloseq') source("http://bioconductor.org/biocLite.R") if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.16") a yes biocLite("phyloseq") source("http://bioconductor.org/biocLite.R") source("https://raw.githubusercontent.com/joey711/phyloseq/master/inst/scripts/installer.R", local = TRUE) yes install_github("beadyallen/MGnifyR") library("devtools") install_github("beadyallen/MGnifyR") library(MGnifyR)
mgnify_client(url = "https://www.ebi.ac.uk/metagenomics/api/v1", username = "Webin-63503", password = "qownstlrqkqhz!1", usecache = T, cache_dir = "/desktop/Mgnify_cache_location", warnings = F, use_memcache = F) mg <- mgnify_client(cache_dir = "/desktop/Mgnify_cache_location") mgnify_query(mg, qtype = "samples", maxhits=10, usecache = T) J <- mgnify_query(mg, qtype = "samples", biome_name = "insecta", maxhits=200, usecache = T) colnames(J) insect_samples = mgnify_query(mg, qtype="samples", biome_name = "insecta", experiment_type = "amplicon", maxhits=200, usecache = T) insect_samples_2 = mgnify_query(mg, qtype="samples", biome_name = "insect", experiment_type = "amplicon", maxhits=200, usecache = T) insect_samples_3 = mgnify_query(mg, qtype="samples", biome_name = "mosquito", experiment_type = "amplicon", maxhits=10, usecache = T) insect_samples_4 = mgnify_query(mg, qtype="samples", sample_name = "insecta", experiment_type = "amplicon", maxhits=10, usecache = T) insect_samples_mosquito = mgnify_query(mg, qtype="samples", environment_feature="Mosquito gut", experiment_type = "amplicon", maxhits=200, usecache = T) insect_samples_mosquito_2 = mgnify_query(mg, qtype="samples", environment_feature="Mosquito gut", maxhits=10, usecache = T) insect_samples_5 = mgnify_query(mg, qtype="runs", biome_name="insecta", maxhits=10, usecache = T) mgnify_query(mg, qtype="samples", biome_name = "insecta", experiment_type = "amplicon", maxhits=10, usecache = T) samp_acc <- insect_samples$accession samp_acc (an_acc <- mgnify_analyses_from_samples(mg, samp_acc)) metadata <- mgnify_get_analyses_metadata(mg, an_acc, usecache=T) head(metadata) colnames(metadata) amplicon_accessions <- metadata$analysis_accession[metadata$'analysis_experiment-type'=="amplicon"] ps <- mgnify_get_analyses_phyloseq(mg, amplicon_accessions) ps@otu_table ps@tax_table
samp_acc <- insect_studies$accession samp_acc (an_acc <- mgnify_analyses_from_samples(mg, samp_acc)) metadata <- mgnify_get_analyses_metadata(mg, an_acc, usecache=T) head(metadata) colnames(metadata) amplicon_accessions <- metadata$analysis_accession[metadata$'analysis_experiment-type'=="amplicon"] ps <- mgnify_get_analyses_phyloseq(mg, amplicon_accessions)
tax_table(ps) otu_table(ps) sample_data(ps) tax_table(ps)
psglom <- tax_glom(normed_ps, "Order") normed_ps <- transform_sample_counts(psglom, function(x) x/sum(x)) plot_bar(normed_ps, fill="Phylum")
ord <- ordinate(ps, "NMDS", "bray") plot_ordination(ps, ord) + geom_point(aes(color=as.numeric(sample_elevation)), size=8) + theme_bw()
mgnify_get_download_urls(client, accessions, accession_type) dl_df <- mgnify_get_download_urls(mg, acc_list, "analyses") head(dl_df)
table(metadata$'analysis_experiment-type' == "amplicon")