EDGE Taxonomy Assignments Visualization

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Documentation for package ‘MetaComp’ version 1.0.1

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load_bwa_assignment Efficiently loads a EDGE-produced BWA taxonomic assignment from a file. An assumption has been made - since bwa/EDGE tables are generated in an automated fashion, they should be properly formatted - thus the code doesn't check for any inconsistencies except for the very file existence. Note however, the unassigned to taxa entries are removed. This implementation fully relies on the read.table function from data.table package gaining performance over traditional R techniques.
load_bwa_assignments Efficiently loads a BWA (or other EDGE-like taxonomic assignment) tables from a list of files. Outputs a named list of assignments.
load_gottcha2_assignment Efficiently loads a GOTTCHA2 (or other EDGE-like taxonomic assignment) table from a file. An assumption has been made - since GOTTCHA2/EDGE tables are generated in an automated fashion, they should be properly formatted - thus the code doesn't check for any inconsistencies except for the very file existence. This implementation fully relies on the read.table function from data.table package gaining performance over traditional R techniques.
load_gottcha2_assignments Efficiently loads a GOTTCHA2 (or other EDGE-like taxonomic assignment) tables from a list of files. Outputs a named list of assignments.
load_gottcha_assignment Efficiently loads a GOTTCHA (or other EDGE-like taxonomic assignment) table from a file. An assumption has been made - since GOTTCHA/EDGE tables are generated in an automated fashion, they should be properly formatted - thus the code doesn't check for any inconsistencies except for the very file existence. This implementation fully relies on the read.table function from data.table package gaining performance over traditional R techniques.
load_gottcha_assignments Efficiently loads a GOTTCHA (or other EDGE-like taxonomic assignment) tables from a list of files. Outputs a named list of assignments.
load_kraken_assignment Efficiently loads a EDGE-produced Kraken taxonomic assignment from a file. An assumption has been made - since Kraken/EDGE tables are generated in an automated fashion, they should be properly formatted - thus the code doesn't check for any inconsistencies except for the very file existence. Note however, the unassigned to taxa entries are removed. This implementation fully relies on the read.table function from data.table package gaining performance over traditional R techniques.
load_kraken_assignments Efficiently loads a GOTTCHA (or other EDGE-like taxonomic assignment) tables from a list of files. Outputs a named list of assignments.
load_metaphlan_assignment Efficiently loads a EDGE-produced Mataphlan taxonomic assignment from a file. An assumption has been made - since Metaphlan/EDGE tables are generated in an automated fashion, they should be properly formatted - thus the code doesn't check for any inconsistencies except for the very file existence. Note however, the unassigned to taxa entries are removed. This implementation fully relies on the read.table function from data.table package gaining performance over traditional R techniques.
load_metaphlan_assignments Efficiently loads a METAPHLAN (or other EDGE-like taxonomic assignment) tables from a list of files. Outputs a named list of assignments.
merge_bwa_assignments Merges two or more BWA-like taxonomical assignments. The input data frames are assumed to have the following columns: LEVEL, TAXA, and ABUNDANCE - these will be used in the merge procedure, all other columns will be ignored.
merge_bwa_counts Merges two or more BWA-like taxonomical assignments. The input data frames are assumed to have the following columns: LEVEL, TAXA, and COUNT - these will be used in the merge procedure, all other columns will be ignored.
merge_gottcha_assignments Merges two or more GOTTCHA-like taxonomical assignments. The input data frames are assumed to have the following columns: LEVEL, TAXA, and ABUNDANCE - these will be used in the merge procedure, all other columns will be ignored.
merge_gottcha_counts Merges two or more GOTTCHA-like taxonomical assignments. The input data frames are assumed to have the following columns: LEVEL, TAXA, and COUNT - these will be used in the merge procedure, all other columns will be ignored.
merge_kraken_assignments Merges two or more Kraken-like taxonomical assignments. The input data frames are assumed to have the following columns: LEVEL, TAXA, and ABUNDANCE - these will be used in the merge procedure, all other columns will be ignored.
merge_metaphlan_assignments Merges two or more Metaphlan-like taxonomical assignments. The input data frames are assumed to have the following columns: LEVEL, TAXA, and ROLLUP - these will be used in the merge procedure, all other columns will be ignored.
plot_bwa_assignment Generates a single column ggplot for a taxonomic assignment table and also outputs a PDF.
plot_gottcha_assignment Generates a single column ggplot for a taxonomic assignment table and also outputs a PDF.
plot_kraken_assignment Generates a single column ggplot for a taxonomic assignment table and also outputs a PDF.
plot_merged_assignment Generates a single column ggplot for a taxonomic assignment table.
plot_metaphlan_assignment Generates a single column ggplot for a taxonomic assignment table and also outputs a PDF.