Index

Symbols

--annotate command line option --annotate_points command line option --color_by COLOR_BY command line option --figsize FIGSIZE FIGSIZE command line option, [1] --font_size FONT_SIZE command line option, [1] --ggplot2_style command line option, [1], [2], [3] --label_padding LABEL_PADDING command line option, [1] --output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN command line option --p1 P1 command line option --p2 P2 command line option --pc_order PC_ORDER command line option --plot_title PLOT_TITLE command line option, [1] --save_calculations SAVE_CALCULATIONS command line option --save_lda_input SAVE_LDA_INPUT command line option, [1] --scale_by SCALE_BY command line option, [1] --scaling_factor SCALING_FACTOR command line option --show_available_metrics command line option --show_significance command line option --stabilize_variance command line option, [1] --x_limits X_LIMITS X_LIMITS command line option --y_limits Y_LIMITS Y_LIMITS command line option --z_angles Z_ANGLES Z_ANGLES command line option, [1] --z_limits Z_LIMITS Z_LIMITS command line option -a {MRA,NMRA,raw}, --analysis_metric {MRA,NMRA,raw} command line option -b GROUP_BY, --group_by GROUP_BY command line option -c CATEGORY, --category CATEGORY command line option -c COLOR_BY, --color_by COLOR_BY command line option -c COLORS, --colors COLORS command line option, [1], [2] -c MAP_CATEGORIES, --map_categories MAP_CATEGORIES command line option -c MAP_CATEGORY, --map_category MAP_CATEGORY command line option -d DIVERSITY [DIVERSITY ...], --diversity DIVERSITY [DIVERSITY ...] command line option -d {2,3}, --dimensions {2,3} command line option, [1] -dm DIST_MATRIX_FILE, --dist_matrix_file DIST_MATRIX_FILE command line option, [1] -e OUTPUT_TRE, --output_tre OUTPUT_TRE command line option -fo FILTER_OTUIDS_FNH, --filter_otuids_fnh FILTER_OTUIDS_FNH command line option -fp FIL_PCT, --fil_pct FIL_PCT command line option -g GROUP_BY [GROUP_BY ...], --group_by GROUP_BY [GROUP_BY ...] command line option -g GROUP_BY, --group_by GROUP_BY command line option, [1] -go GEXF_OUT, --gexf_out GEXF_OUT command line option -h, --help command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25] -i ASSIGNED_TAXONOMY_FN, --assigned_taxonomy_fn ASSIGNED_TAXONOMY_FN command line option -i BIOM_FP, --biom_fp BIOM_FP command line option, [1] -i COORD_FP, --coord_fp COORD_FP command line option -i INPUT_ASSIGNED_TAXONOMY, --input_assigned_taxonomy INPUT_ASSIGNED_TAXONOMY command line option -i INPUT_BIOM_FP, --input_biom_fp INPUT_BIOM_FP command line option, [1] -i INPUT_FASTA_FN, --input_fasta_fn INPUT_FASTA_FN command line option, [1] -i INPUT_FNA [INPUT_FNA ...], --input_fna INPUT_FNA [INPUT_FNA ...] command line option -i OTU_ID_FP, --otu_id_fp OTU_ID_FP command line option -i OTU_MAP, --otu_map OTU_MAP command line option -i OTU_TABLE, --otu_table OTU_TABLE command line option, [1], [2] -i REP_SET_FP, --rep_set_fp REP_SET_FP command line option -i SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN command line option -ids OTU_IDS_FP, --otu_ids_fp OTU_IDS_FP command line option, [1]

-k SAMPLES_TO_KEEP_FP, --samples_to_keep_fp SAMPLES_TO_KEEP_FP command line option -L {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s} command line option -l {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s} command line option, [1] -m MAP_FILE, --map_file MAP_FILE command line option -m MAP_FP, --map_fp MAP_FP command line option, [1], [2] -m MAPPING, --mapping MAPPING command line option, [1], [2] -m MAPPING_FN, --mapping_fn MAPPING_FN command line option -n JOB_NAME, --job_name JOB_NAME command line option -n NON_UNIQUE_OTU_MATRIX, --non_unique_otu_matrix NON_UNIQUE_OTU_MATRIX command line option -n NON_UNIQUE_OUTPUT_FILE, --non_unique_output_file NON_UNIQUE_OUTPUT_FILE command line option -n NUM_OUTPUT_FILES, --num_output_files NUM_OUTPUT_FILES command line option -o ASSIGNED_TAXONOMY_FP, --assigned_taxonomy_fp ASSIGNED_TAXONOMY_FP command line option -o CONDENSED_SEQS_OTUS_FILE, --condensed_seqs_otus_file CONDENSED_SEQS_OTUS_FILE command line option -o OUT_DIR, --out_dir OUT_DIR command line option -o OUT_FP, --out_fp OUT_FP command line option, [1] -o OUTPUT_BIOM_FP, --output_biom_fp OUTPUT_BIOM_FP command line option -o OUTPUT_CSV_FP, --output_csv_fp OUTPUT_CSV_FP command line option -o OUTPUT_DIR, --output_dir OUTPUT_DIR command line option, [1], [2] -o OUTPUT_FILTERED_REP_SET_FN, --output_filtered_rep_set_fn OUTPUT_FILTERED_REP_SET_FN command line option -o OUTPUT_FN, --output_fn OUTPUT_FN command line option -o OUTPUT_FP, --output_fp OUTPUT_FP command line option, [1] -o OUTPUT_ITOL_TABLE, --output_itol_table OUTPUT_ITOL_TABLE command line option -o OUTPUT_OTU_MAP_FP, --output_otu_map_fp OUTPUT_OTU_MAP_FP command line option -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX command line option -o OUTPUT_PRUNED_OTUS_FN, --output_pruned_otus_fn OUTPUT_PRUNED_OTUS_FN command line option -o REPSET_OUT_FP, --repset_out_fp REPSET_OUT_FP command line option -od OUTPUT_DIR, --output_dir OUTPUT_DIR command line option -ot OTU_TABLE, --otu_table OTU_TABLE command line option -p IMAGE_TYPE, --image_type IMAGE_TYPE command line option -p PERCENT_OF_SAMPLES, --percent_of_samples PERCENT_OF_SAMPLES command line option -p PREFIX, --prefix PREFIX command line option -p PRUNED_OUTPUT_FILE, --pruned_output_file PRUNED_OUTPUT_FILE command line option -pc PCOA_FP, --pcoa_fp PCOA_FP command line option -q QUALITY_FN, --quality_fn QUALITY_FN command line option -r REP_SET_FN, --rep_set_fn REP_SET_FN command line option, [1] -r REPSET_FP, --repset_fp REPSET_FP command line option -r REVERSE, --reverse REVERSE command line option -s PERCENT_OF_SEQUENCES, --percent_of_sequences PERCENT_OF_SEQUENCES command line option -s POINT_SIZE, --point_size POINT_SIZE command line option -s SAVE_AS, --save_as SAVE_AS command line option, [1] -s SEQS_OTUS, --seqs_otus SEQS_OTUS command line option -s SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN command line option -t ID_TO_TAXONOMY_FN, --id_to_taxonomy_fn ID_TO_TAXONOMY_FN command line option -t ID_TO_TAXONOMY_FP, --id_to_taxonomy_fp ID_TO_TAXONOMY_FP command line option -t INPUT_TREE, --input_tree INPUT_TREE command line option -t TAXONOMY_FP, --taxonomy_fp TAXONOMY_FP command line option -t TITLE, --title TITLE command line option -t WALLTIME, --walltime WALLTIME command line option -t, --test command line option -u UNIQUE_OTUS_FN, --unique_otus_fn UNIQUE_OTUS_FN command line option -v, --verbose command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] -w STATS_OUT_FNH, --stats_out_fnh STATS_OUT_FNH command line option

A

ax: command line option

B

biom_file command line option biomf: command line option, [1], [2], [3]

biomfile: command line option

C

cat_name command line option categories: command line option category_column command line option color: command line option command line option --annotate --annotate_points --color_by COLOR_BY --figsize FIGSIZE FIGSIZE, [1] --font_size FONT_SIZE, [1] --ggplot2_style, [1], [2], [3] --label_padding LABEL_PADDING, [1] --output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN --p1 P1 --p2 P2 --pc_order PC_ORDER --plot_title PLOT_TITLE, [1] --save_calculations SAVE_CALCULATIONS --save_lda_input SAVE_LDA_INPUT, [1] --scale_by SCALE_BY, [1] --scaling_factor SCALING_FACTOR --show_available_metrics --show_significance --stabilize_variance, [1] --x_limits X_LIMITS X_LIMITS --y_limits Y_LIMITS Y_LIMITS --z_angles Z_ANGLES Z_ANGLES, [1] --z_limits Z_LIMITS Z_LIMITS -L {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s} -a {MRA,NMRA,raw}, --analysis_metric {MRA,NMRA,raw} -b GROUP_BY, --group_by GROUP_BY -c CATEGORY, --category CATEGORY -c COLORS, --colors COLORS, [1], [2] -c COLOR_BY, --color_by COLOR_BY -c MAP_CATEGORIES, --map_categories MAP_CATEGORIES -c MAP_CATEGORY, --map_category MAP_CATEGORY -d DIVERSITY [DIVERSITY ...], --diversity DIVERSITY [DIVERSITY ...] -d {2,3}, --dimensions {2,3}, [1] -dm DIST_MATRIX_FILE, --dist_matrix_file DIST_MATRIX_FILE, [1] -e OUTPUT_TRE, --output_tre OUTPUT_TRE -fo FILTER_OTUIDS_FNH, --filter_otuids_fnh FILTER_OTUIDS_FNH -fp FIL_PCT, --fil_pct FIL_PCT -g GROUP_BY [GROUP_BY ...], --group_by GROUP_BY [GROUP_BY ...] -g GROUP_BY, --group_by GROUP_BY, [1] -go GEXF_OUT, --gexf_out GEXF_OUT -h, --help, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20], [21], [22], [23], [24], [25] -i ASSIGNED_TAXONOMY_FN, --assigned_taxonomy_fn ASSIGNED_TAXONOMY_FN -i BIOM_FP, --biom_fp BIOM_FP, [1] -i COORD_FP, --coord_fp COORD_FP -i INPUT_ASSIGNED_TAXONOMY, --input_assigned_taxonomy INPUT_ASSIGNED_TAXONOMY -i INPUT_BIOM_FP, --input_biom_fp INPUT_BIOM_FP, [1] -i INPUT_FASTA_FN, --input_fasta_fn INPUT_FASTA_FN, [1] -i INPUT_FNA [INPUT_FNA ...], --input_fna INPUT_FNA [INPUT_FNA ...] -i OTU_ID_FP, --otu_id_fp OTU_ID_FP -i OTU_MAP, --otu_map OTU_MAP -i OTU_TABLE, --otu_table OTU_TABLE, [1], [2] -i REP_SET_FP, --rep_set_fp REP_SET_FP -i SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN -ids OTU_IDS_FP, --otu_ids_fp OTU_IDS_FP, [1] -k SAMPLES_TO_KEEP_FP, --samples_to_keep_fp SAMPLES_TO_KEEP_FP -l {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}, [1] -m MAPPING, --mapping MAPPING, [1], [2] -m MAPPING_FN, --mapping_fn MAPPING_FN -m MAP_FILE, --map_file MAP_FILE -m MAP_FP, --map_fp MAP_FP, [1], [2] -n JOB_NAME, --job_name JOB_NAME -n NON_UNIQUE_OTU_MATRIX, --non_unique_otu_matrix NON_UNIQUE_OTU_MATRIX -n NON_UNIQUE_OUTPUT_FILE, --non_unique_output_file NON_UNIQUE_OUTPUT_FILE -n NUM_OUTPUT_FILES, --num_output_files NUM_OUTPUT_FILES -o ASSIGNED_TAXONOMY_FP, --assigned_taxonomy_fp ASSIGNED_TAXONOMY_FP -o CONDENSED_SEQS_OTUS_FILE, --condensed_seqs_otus_file CONDENSED_SEQS_OTUS_FILE -o OUTPUT_BIOM_FP, --output_biom_fp OUTPUT_BIOM_FP -o OUTPUT_CSV_FP, --output_csv_fp OUTPUT_CSV_FP -o OUTPUT_DIR, --output_dir OUTPUT_DIR, [1], [2] -o OUTPUT_FILTERED_REP_SET_FN, --output_filtered_rep_set_fn OUTPUT_FILTERED_REP_SET_FN -o OUTPUT_FN, --output_fn OUTPUT_FN -o OUTPUT_FP, --output_fp OUTPUT_FP, [1] -o OUTPUT_ITOL_TABLE, --output_itol_table OUTPUT_ITOL_TABLE -o OUTPUT_OTU_MAP_FP, --output_otu_map_fp OUTPUT_OTU_MAP_FP -o OUTPUT_PREFIX, --output_prefix OUTPUT_PREFIX -o OUTPUT_PRUNED_OTUS_FN, --output_pruned_otus_fn OUTPUT_PRUNED_OTUS_FN -o OUT_DIR, --out_dir OUT_DIR -o OUT_FP, --out_fp OUT_FP, [1] -o REPSET_OUT_FP, --repset_out_fp REPSET_OUT_FP -od OUTPUT_DIR, --output_dir OUTPUT_DIR -ot OTU_TABLE, --otu_table OTU_TABLE -p IMAGE_TYPE, --image_type IMAGE_TYPE -p PERCENT_OF_SAMPLES, --percent_of_samples PERCENT_OF_SAMPLES -p PREFIX, --prefix PREFIX -p PRUNED_OUTPUT_FILE, --pruned_output_file PRUNED_OUTPUT_FILE -pc PCOA_FP, --pcoa_fp PCOA_FP -q QUALITY_FN, --quality_fn QUALITY_FN -r REPSET_FP, --repset_fp REPSET_FP -r REP_SET_FN, --rep_set_fn REP_SET_FN, [1] -r REVERSE, --reverse REVERSE -s PERCENT_OF_SEQUENCES, --percent_of_sequences PERCENT_OF_SEQUENCES -s POINT_SIZE, --point_size POINT_SIZE -s SAVE_AS, --save_as SAVE_AS, [1] -s SEQS_OTUS, --seqs_otus SEQS_OTUS -s SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN -t ID_TO_TAXONOMY_FN, --id_to_taxonomy_fn ID_TO_TAXONOMY_FN -t ID_TO_TAXONOMY_FP, --id_to_taxonomy_fp ID_TO_TAXONOMY_FP -t INPUT_TREE, --input_tree INPUT_TREE -t TAXONOMY_FP, --taxonomy_fp TAXONOMY_FP -t TITLE, --title TITLE -t WALLTIME, --walltime WALLTIME -t, --test -u UNIQUE_OTUS_FN, --unique_otus_fn UNIQUE_OTUS_FN -v, --verbose, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] -w STATS_OUT_FNH, --stats_out_fnh STATS_OUT_FNH Returns an opened file for appropriate usage. ax: biom_file biomf:, [1], [2], [3] biomfile: cat_name categories: category_column color: condition_column core_fp: d: data: fastaFNH:, [1] file_data, [1] fill_bt: fn: fnh: header:, [1] idtaxFNH: imap: in_corr_mat input_biom_fnh input_biom_fp items: job_scripts level: mapFNH:, [1] mapping_file, [1] mapping_fnh mode: otuIDs: output_biom_fnh p: pick_otus_results rel_abd:, [1] return:, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20] sampleIDs:, [1] sample_abd:, [1] tax: title: unifrac:, [1] unifracFN:

condition_column command line option core_fp: command line option

D

d: command line option

data: command line option

F

fastaFNH: command line option, [1] file_data command line option, [1] fill_bt: command line option

fn: command line option fnh: command line option

H

header: command line option, [1]

I

idtaxFNH: command line option imap: command line option in_corr_mat command line option

input_biom_fnh command line option input_biom_fp command line option items: command line option

J

job_scripts command line option

L

level: command line option

M

mapFNH: command line option, [1] mapping_file command line option, [1]

mapping_fnh command line option mode: command line option

O

otuIDs: command line option

output_biom_fnh command line option

P

p: command line option

pick_otus_results command line option

R

rel_abd: command line option, [1] return: command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15], [16], [17], [18], [19], [20]

Returns an opened file for appropriate usage. command line option

S

sample_abd: command line option, [1]

sampleIDs: command line option, [1]

T

tax: command line option

title: command line option

U

unifrac: command line option, [1]

unifracFN: command line option