Usage:
apav geneBatch --gff <GFF_file> --bamdir <BAM_dir> --pheno <phenotype_file> --out <res_prefix> [options]
| Necessary input: | ||
| -i, --gff | file | GFF file. |
| -o, --out | string | Output file prefix |
| -b, --bamdir | dir | The directory contains mapping results (sorted '.bam' files). |
| --pheno | file | Phenotype file. |
| Options for elements in the upstream and downstream region: | ||
| --chrl | file | Chromosome length file. |
| --up_n | int | Number of bin(s) in gene upstream region. (Default:0) |
| --up_bin | int | The interval width of bin(s) in gene upstream region. (Default:100) |
| --down_n | int | Number of bin(s) in gene downstream region. (Default:0) |
| --down_bin | int | The interval width of bin(s) in gene downstream region. (Default:100) |
| Options for coverage calculation: | ||
| --rep | type | Representative transcript selection methods: "cdslen": using the transcript with the longest CDS region; "len": using the longest transcript; "highcov": using the transcript with the highest coverage; "none": using gene body region; "all": considering all transcript reigon. (Default:"cdslen") |
| --mincov | int | Depth threshold. (Default:1) |
| --rmele | Remove analysis on elements. | |
| --merge | Merge neighboring elements with the same coverage(all 0 or all 1). | |
| --thread | int | Thread number. |
| Options for PAV Determination: | ||
| --method | type | Method of determination: "fixed" or "adaptive". (Default:"fixed") |
| --thre | float | Coverage threshold. (Default:0.5) |
| --mina | float | Min absence. (Default:0.1) |
| --iter | int | Maximum number of iterations. (Default:100) |
| Options for the tracks in genome browser in PAV report: | ||
| --fa | file | Fasta file of reference genome. |
| --slice | Extract the bam file of the target regions, otherwise make symbolic links for the raw bam file. | |
| Options for the phenotype association analysis: | ||
| --p_threshold | numeric | The filter threshold for p_value/p_adjusted. (Default: 0.01) |
| --adjust_p | Adjust p_value. | |
| Other Options: | ||
| --fam | file | Gene family table. |
| --focused_pheno | string | The phenotype in focus. |
| --example_n | int | The number of examples used to show figures drawn by'pavPlotPhenoVio/pavPlotPhenoBar' commands and 'elePlotCov/elePlotPAV/elePlotDepth' commands. (Default:5) |
| -h, --help | Print usage page. | |
Usage:
apav generalBatch --bed <BED_file> --bamdir <BAM_dir> --pheno <phenotype_file> --out <res_prefix> [options]
| Necessary input: | ||
| -i, --gff | file | GFF file. |
| -o, --out | string | Output file prefix. |
| -b, --bamdir | dir | The directory contains mapping results (sorted '.bam' files). |
| --pheno | file | Phenotype file. |
| Options for coverage calculation: | ||
| --mincov | int | Depth threshold. (Default:1) |
| --rmele | Remove analysis on elements. | |
| --merge | Merge neighboring elements with the same coverage (all 0 or all 1). | |
| --thread | Thread number. | |
| Options for PAV Determination: | ||
| --method | type | Method of determination: "fixed" or "adaptive". (Default:"fixed") |
| --thre | float | Coverage threshold. (Default:0.5) |
| --mina | float | Min absence. (Default:0.1) |
| --iter | int | Maximum number of iterations. (Default:100) |
| Options for the tracks in genome browser: | ||
| --fa | file | Fasta file of reference genome. |
| Options for the phenotype association analysis: | ||
| --p_threshold | numeric | The filter threshold for p_value/p_adjusted. (Default: 0.01) |
| --adjust_p | Adjust p_value. | |
| Other Options: | ||
| --focused_pheno | string | The phenotype in focus. |
| --example_n | int | The number of examples used to show figures drawn by 'pavPlotPhenoVio/pavPlotPhenoBar' commands and 'elePlotCov/elePlotPAV/elePlotDepth' commands. |
| -h, --help | Print usage page. | |
Usage:
apav gff2bed --gff <gff_file> [options]
| Necessary input: | ||
| -i, --gff | file | Gene annotations in a GFF file. |
| Options: | ||
| -o, --out | string | Output file name. |
| --chrl | file | Chromosome length file. |
| --up_n | int | Number of bin(s) in gene upstream region. (Default:0) |
| --up_bin | int | The interval width of bin(s) in gene upstream region. (Default:100) |
| --down_n | int | Number of bin(s) in gene downstream region. (Default:0) |
| --down_bin | int | The interval width of bin(s) in gene downstream region. (Default:100) |
| -h, --help | Print usage page. | |
Warning: '--chrl' is required when setting 'up_n'&'up_bin' or 'down_n'&'down_bin'
Usage:
apav staCov --bed <BED_file> --bamdir <bam_dir> [options]
| Necessary input description: | ||
| -i, --bed | file | Annotation of target regions in a BED file. |
| -b, --bamdir | dir | The directory contains mapping results (sorted '.bam' files). |
| Options: | ||
| -o, --out | string | Output file prefix. |
| --asgene | Treating target regions as genes. | |
| --rep | type | Representative transcript selection methods: "cdslen": using the transcript with the longest CDS region; "len": using the longest transcript; "highcov": using the transcript with the highest coverage; "none": using gene body region; "all": considering all transcript reigon. (Default:"cdslen") |
| --mincov | int | Depth threshold. (Default:1) |
| --rmele | Remove analysis on elements. | |
| --merge | Merge neighboring elements with the same coverage(all 0 or all 1). | |
| --thread | int | Thread number. |
| -h, --help | Print usage page. | |
Warning:
Usage:
apav mergeElecov --elecov <elecov_file> --out <out_file_name> [options]
| Necessary input: | ||
| -i, --elecov | file | Element coverage file. |
| Options: | ||
| --asgene | Treating elements as gene elements. | |
| -o, --out | string | Output file name. |
| -h, --help | Print usage page. | |
Usage:
apav covPlotHeat --cov <cov_file> -o <figure_name> [options]
| Necessary input: | ||
| -i, --cov | file | Coverage file. |
| Options: | ||
| -p, --pheno | file | Phenotype file. |
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --cov_colors | colors | The colors for coverage, separated by commas. (Default: 'white,#F8766D') |
| --pheno_info_color_list | key=value | The colors for phenotype annotations. (eg: 'gender=blue,green') |
| --border | Draw border for main heatmap. | |
| --cluster_rows | Perform clustering on rows. | |
| --clustering_distance_rows | type | Method of measuring distance when clustring on rows,choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_rows | type | Method to perform hierarchical clustering on rows, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'.(Default: 'complete') |
| --row_dend_side | type | The position of the row dendrogram, 'left' or 'right'. |
| --row_dend_width | numeric | The width of the row dendrogram. |
| --row_sorted | string | The sorted row names, separated by commas. It doesn't work when '--cluster_rows' is used. |
| --show_row_names | Show row names. | |
| --row_names_side | type | The position of row names, 'left' or 'right'. |
| --row_names_size | numeric | The size of row names. |
| --row_names_rot | numeric | The rotation of row names. |
| --cluster_columns | Perform clustering on columns. | |
| --clustering_distance_columns | type | Method of measuring distance when clustring on columns. choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_columns | type | Method to perform hierarchical clustering on columns. choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --column_dend_side | type | The position of the column dendrogram, 'top' or 'bottom'. |
| --column_dend_height | numeric | The height of the column dendrogram. |
| --column_sorted | string | The sorted column names, separated by commas. It doesn't work when '--cluster_columns'. |
| --show_column_names | Show column names. | |
| --column_names_side | type | The position of column names, 'top' or 'column'. |
| --column_names_size | numeric | The size of column names. |
| --column_names_rot | numeric | The rotation of column names. |
| --anno_param_row_pheno | key=value | Parameters for the phenotype annotation, including 'show' type ('T','F'), 'width' numeric, 'border' type ('T', 'F'), 'name_size' numeric, 'name_rot numeric, 'name_side' type ('top', 'bottom'). |
| --anno_param_column_region | key=value | Parameters for the region annotation, including 'show' type ('T', 'F'), 'height' numeric, 'border' type ('T', 'F'), 'name_size' numeric, 'name_rot' numeric, 'name_side' type ('left', 'right'). |
| --anno_param_row_stat | key=value | Parameters for the stat annotation of rows, including 'show' type ('T','F'), 'width' numeric, 'border' type ('T','F'), 'title' string, 'title_size' numeric, 'title_rot' numeric, 'title_side' type ('top', 'bottom'), 'axis_side' type ('top', 'bottom'), 'axis_labels_size' numeric. |
| --anno_param_column_stat | key=value | Parameters for the stat annotation of columns, including 'show' type ('T','F'), 'height' numeric, 'border' type ('T','F'), 'title' string, 'title_size' numeric, 'title_rot' numeric, 'title_side' type ('left', 'right'), 'axis_side' type ('left', 'right'), 'axis_labels_size' numeric. |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_title | string | The text for the legend title. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| --legend_grid_size | numeric | The size of legend grid. |
| --use_raster | Render the heatmap body as a raster image. | |
| -h, --help | Print usage page. | |
Warning: --pheno_info_color_list --anno_param_row_phen --anno_param_column_region --anno_param_row_stat --anno_param_column_stat can be added multiple times. eg: --anno_param_row_pheno show=T --anno_param_row_pheno width=5 --anno_param_row_pheno name_rot=90
Usage:
apav callPAV --cov <cov_file> --pheno <phenotype_file> [options]
| Necessary input: | ||
| -i, --cov | file | Coverage file. |
| --pheno | file | Phenotype file. |
| Options: | ||
| -o, --out | string | Output file prefix. |
| --method | type | Method of determination: "fixed" or "adaptive". (Default:"fixed") |
| --thre | float | Coverage threshold. (Default:0.5) |
| --mina | float | Min absence. (Default:0.1) |
| --iter | int | Maximum number of iterations. (Default:100) |
| Options for the tracks in genome browser: | ||
| --fa | file | Fasta file of reference genome. |
| --gff | file | GFF file is used to add annotation tracks in the genome browser. |
| -b, --bamdir | dir | The directory contains mapping results (sorted '.bam' files). |
| --slice | Extract the bam file of the target regions, otherwise make symbolic links for the raw bam file. | |
| -h, --help | Print usage page. | |
Usage:
apav gfamPAV --pav <pav_file> --fam <gene_family_info> [option]
| Necessary input description: | ||
| -i, --pav | file | Gene PAV file. |
| --fam | file | Gene family table. |
| Options: | ||
| -o, --out | string | Output file name. |
| -h, --help | Print usage page. | |
Usage:
apav mergeElePAV --pav <elecov_file> [option]
| Necessary input: | ||
| -i, --pav | file | Element PAV file. |
| Options: | ||
| -o, --out | string | Output file name. |
| -h, --help | Print usage page. | |
Usage:
apav pavSize --pav <pav_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file. |
| Options: | ||
| -o, --out | string | Output file name. |
| -n | int | Specifies the number of random sampling times. (Default:100) |
| -g, --group | file | Group file for samples. |
| -h, --help | Print usage page. | |
Usage:
apav pavPlotSize -i <estimation_output_file> [options]
| Necessary input: | ||
| -i, --size | file | Result file produced by command 'apav pavSize'. |
| Options: | ||
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --chart_type | type | Chart type. It should be one of 'errorbar', 'jitter' and 'ribbon'. (Default:'ribbon') |
| --data_type | type | The type of data displayed. It should be 'count' or 'change'. (Default: 'count') |
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --x_title | string | The text for the x-axis title. |
| --y_title | string | The text for the y-axis title. |
| --x_title_size | numeric | The size of x-axis title. |
| --y_title_size | numeric | The size of y-axis title. |
| --x_breaks | string | The break values on the x-axis, separated by commas. (eg: '1,5,10') |
| --y_breaks | string | The break values on the y-axis, separated by commas. (eg: '10,20,30') |
| --x_text_size | numeric | The size of tick labels on x-axis. |
| --y_text_size | numeric | The size of tick labels on x-axis. |
| --hide_legend | Hide the legend. | |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'left', 'right'.(Default: right) |
| --legend_title | string | The text for the legend title. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| --errorbar_width | numeric | The relative width of errorbar, ranging from 0 to 1. |
| --errorbar_size | numeric | The size of errorbar. |
| --errorbar_color | colors | The colors for errorbar, separated by commas. |
| --errorbar_alpha | numeric | The opacity of errorbar, ranging from 0 to 1. |
| --errorbar_point_size | numeric | The size of point representing the mean value. |
| --errorbar_point_color | colors | The colors for point representing the mean value, separated by commas. |
| --jitter_width | numeric | The numeric vector giving the relative width of jittered points, ranging from 0 to 1. |
| --jitter_size | numeric | The size of jittered points. |
| --jitter_color | colors | The colors for jittered points, separated by commas. |
| --jitter_alpha | numeric | The opacity of jittered points, ranging from 0 to 1. |
| --jitter_point_size | numeric | The size of point representing the mean value. |
| --jitter_point_color | colors | The colors for point representing the mean value, separated by commas. |
| --path_size | numeric | The size of path. |
| --path_color | colors | The colors for path, separated by commas. |
| --ribbon_fill | colors | The colors for ribbon, separated by commas. |
| --ribbon_alpha | numeric | The opacity of ribbon, ranging from 0 to 1. |
| -h, --help | Print usage page. | |
Usage:
apav pavPlotStat --pav <pav_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| Options: | ||
| --pheno | file | Phenotype file. |
| --add_pheno_info | string | Group the samples by this phenotype |
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --color | color | The color for halfviolin. |
| --pheno_info_colors | colors | The colors for the phenotype groups, separated by commas. |
| --x_text_size | numeric | The size of tick labels on the x-axis. |
| --y_text_size | numeric | The size of tick labels on the y-axis. |
| --x_title_size | numeric | The size of x-axis title. |
| --y_title_size | numeric | The size of y-axis title. |
Usage:
apav pavPlotHeat --pav <pav_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| Options: | ||
| -p, --pheno | file | Phenotype file. |
| -o, --out | string | Figure name. |
| --rm_softcore | Exclude `soft-core` when determining the classification of the region. | |
| --rm_private | Exclude `private` when determining the classification of the region. | |
| --softcore_loss_rate | numeric | Loss rate. |
| --use_binomial | Use binomial test when determining `soft-core`. | |
| --softcore_p_value | numeric | P-value (binomial test). |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --pav_colors | colors | The colors for presence and absence, separated by commas. |
| --type_colors | colors | The colors for classifications of the region, separated by commas. |
| --pheno_info_color_list | key=value | The colors for phenotype annotations. (eg: 'gender=blue,green') |
| --hide_border | Hide border of blocks in heatmap. | |
| --block_name_size | numeric | The size of block name. |
| --block_name_rot | numeric | The rotation of block name. |
| --cluster_rows | Perform clustering on rows. | |
| --clustering_distance_rows | type | Method of measuring distance when clustring on rows,choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_rows | type | Method to perform hierarchical clustering on rows, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --row_dend_side | type | The position of the row dendrogram, 'left' or 'right'. |
| --row_dend_width | numeric | The width of the row dendrogram. |
| --row_sorted | string | The sorted row names, separated by commas. It doesn't work when '--cluster_rows' is used. |
| --show_row_names | Show row names. | |
| --row_names_side | type | The position of row names, 'left' or 'right'. |
| --row_names_size | numeric | The size of row names. |
| --row_names_rot | numeric | The rotation of row names. |
| --cluster_columns | Perform clustering on columns. | |
| --clustering_distance_columns | type | Method of measuring distance when clustring on columns, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_columns | type | Method to perform hierarchical clustering on columns, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --column_dend_side | type | The position of the column dendrogram, 'top' or 'bottom'. |
| --column_dend_height | numeric | The height of the column dendrogram. |
| --column_sorted | string | The sorted column names, separated by commas. It doesn't work when '--cluster_columns'. |
| --show_column_names | Show column names. | |
| --column_names_side | type | The position of column names, 'top' or 'column'. |
| --column_names_size | numeric | The size of column names. |
| --column_names_rot | numeric | The rotation of column names. |
| --anno_param_row_pheno | key=value | Parameters for the phenotype annotation, including 'show' type ('T','F'), 'width' numeric, 'border' type ('T', 'F'), 'name_size' numeric, 'name_rot numeric, 'name_side' type ('top', 'bottom'). |
| --anno_param_column_region | key=value | Parameters for the region annotation, including 'show' type ('T', 'F'), 'height' numeric, 'border' type ('T', 'F'), 'name_size' numeric, 'name_rot' numeric, 'name_side' type ('left', 'right'). |
| --anno_param_row_stat | key=value | Parameters for the stat annotation of rows, including 'show' type ('T','F'), 'width' numeric, 'border' type ('T','F'), 'title' string, 'title_size' numeric, 'title_rot' numeric, 'title_side' type ('top', 'bottom'), 'axis_side' type ('top', 'bottom'), 'axis_labels_size' numeric. |
| --anno_param_column_stat | key=value | Parameters for the stat annotation of columns, including 'show' type ('T','F'), 'height' numeric, 'border' type ('T','F'), 'title' string, 'title_size' numeric, 'title_rot' numeric, 'title_side' type ('left', 'right'), 'axis_side' type ('left', 'right'), 'axis_labels_size' numeric. |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_title | string | The text for the legend title. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| --legend_grid_size | numeric | The size of legend grid. |
| --use_raster | Render the heatmap body as a raster image. | |
| -h, --help | Print usage page. | |
Warning: --pheno_info_color_list --anno_param_row_phen --anno_param_column_region --anno_param_row_stat --anno_param_column_stat can be added multiple times. eg: --anno_param_row_pheno show=T --anno_param_row_pheno width=5 --anno_param_row_pheno name_rot=90
Usage:
apav pavPlotBar --pav <pav_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| Options: | ||
| --pheno | file | Phenotype file. |
| --add_pheno_info | string | Group the samples by this phenotype. |
| -o, --out | string | Figure name. |
| --rm_softcore | Exclude `soft-core` when determining the classification of the region. | |
| --rm_private | Exclude `private` when determining the classification of the region. | |
| --softcore_loss_rate | numeric | Loss rate. |
| --use_binomial | Use binomial test when determining `soft-core`. | |
| --softcore_p_value | numeric | P-value (binomial test). |
| --clustering_distance | type | Method to measure distance, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'. (Default: 'euclidean') |
| --clustering_method | type | Method to perform hierarchical clustering, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --show_relative | Show relative value. | |
| --type_colors | colors | The colors for classifications of the region, separated by commas. |
| --phen_info_colors | colors | The colors for the phenotype groups, separated by commas. |
| --bar_width | numeric | The relative width of bars, ranging from 0 to 1. |
| --sample_name_size | numeric | The size of sample names. |
| --legend_side | type | The position of legend ('top', 'bottom', 'right', 'left'). |
| --legend_title | string | The text for the legend title. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| --dend_width | numeric | The relative width of dendrogram, ranging from 0 to 1. |
| --name_width | numeric | The relative width of sample names, ranging from 0 to 1. |
| -h, --help | Print usage. | |
Usage:
apav pavPCA --pav <pav_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| Options: | ||
| --pheno | file | Phenotype file. |
| --add_pheno_info | string | Add phenotype information. |
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --pheno_info_colors | colors | The colors for the phenotype groups, separated by commas. |
| --axis_text_size | numeric | The size of tick labels on axis. |
| --axis_title_size | numeric | The size of axis title. |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_text_size | numeric | The size of legend item labels. |
| --legend_title_size | numeric | The size of legend title. |
| -h, --help | Print usage. | |
Usage:
apav pavCluster --pav <pav_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| Options: | ||
| --pheno | file | Phenotype file. |
| --add_pheno_info | string | Group the samples by this phenotype. |
| -o, --out | string | Figure name. |
| --clustering_distance | type | Method to measure distance, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'. (Default: 'euclidean') |
| --clustering_method | type | Method to perform hierarchical clustering, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --pheno_info_colors | colors | The colors for the phenotype groups, separated by commas. |
| --sample_name_size | numeric | The size of labels. |
| --mult | numeric | A numebr of multiplicative range expansion factors. |
| --legend_side | type | The position of legend ('top', 'bottom', 'right', 'left'). |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| -h, --help | Print usage. | |
Usage:
apav pavStaPheno --pav <pav_file> --pheno <phenotype_file> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file. |
| -p, --pheno | file | Phenotype file |
| Options: | ||
| -o, --out | string | Output file name. |
| --p_adjust_method | type | The adjustment methods,choosing from 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'.(Default: fdr) |
| --parallel_n | int | The number of CPU cores used for parallel computing. |
| -h, --help | Print usage page. | |
Usage:
apav pavPlotPhenoHeat --pav <pav_file> --pheno_res <phenotype_association_result> [options]
| Necessary input: | ||
| --pav | file | PAV file produced by command 'apav callPAV'. |
| --pheno_res | file | Phenotype file. |
| Options: | ||
| -o, --out | string | Figure name. |
| --p_threshold | numeric | The threshold of p_value/p_adjusted. (Default: 0.01) |
| --adjust_p | Adjust p_value. | |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --only_show_significant | Only show p_value/p_adjusted that satisfies the condition. | |
| --flip | Flip the cartesian coordinates. | |
| --p_colors | colors | The colors for p_value/p_adjusted, separated by commas. |
| --na_col | color | The color for NA values. |
| --cell_border_color | color | The color for the border of cells. |
| --region_info_color_list | colors | The colors for region annotations. (eg: 'chr=black,red') |
| --cluster_rows | Perform clustering on rows. | |
| --clustering_distance_rows | type | Method of measuring distance when clustring on rows, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_rows | type | Method to perform hierarchical clustering on rows, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --row_dend_side | type | The position of the row dendrogram, 'left' or 'right'. |
| --row_dend_width | numeric | The width of the row dendrogram. |
| --row_sorted | string | The sorted row names, separated by commas. It doesn't work when '--cluster_rows' is used. |
| --show_row_names | Show row names. | |
| --row_names_side | type | The position of row names, 'left' or 'right'. |
| --row_names_size | numeric | The size of row names. |
| --row_names_rot | numeric | The rotation of row names. |
| --cluster_columns | Perform clustering on columns. | |
| --clustering_distance_columns | type | Method of measuring distance when clustring on columns, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_columns | type | Method to perform hierarchical clustering on columns, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --column_dend_side | type | The position of the column dendrogram, 'top' or 'bottom'. |
| --column_dend_height | numeric | The height of the column dendrogram. |
| --column_sorted | string | The sorted column names, separated by commas. It doesn't work when '--cluster_columns'. |
| --show_column_names | Show column names. | |
| --column_names_side | type | The position of column names, 'top' or 'column'. |
| --column_names_size | numeric | The size of column names. |
| --column_names_rot | numeric | The rotation of column names. |
| --anno_param_region | key=value | Parameters for the region annotation, including 'show' type ('T', 'F'), 'width' numeric, 'border' type ('T', 'F'), 'name_size' numeric, 'name_rot' numeric, 'name_side' type ('left', 'right'). |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_title | string | The text for the legend title. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| --legend_grid_size | numeric | The size of legend grid. |
| -h, --help | Print usage. | |
Usage:
apav pavPlotPhenoBlock --pav <pav_file> --pheno <phenotype file> --pheno_res <phenotype_association_result> --phen_name <phenotype name> [options]
| Necessary input: | ||
| -i, --pav | string | PAV file produced by command 'apav callPAV'. |
| --pheno | file | Phenotype file. |
| --pheno_res | string | The result of phenotype association result produced by 'apav pavStaPheno'. |
| --pheno_name | string | Phenotype name. |
| Options: | ||
| -o, --out | string | Figure name. |
| --p_threshold | numeric | The threshold of p_value/p_adjusted. (Default: 0.01) |
| --adjust_p | Adjust p_value. | |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --only_show_significant | Only show p_value/p_adjusted that satisfies the condition. | |
| --flip | Flip the cartesian coordinates. | |
| --per_colors | colors | The colors for absence percentage, separated by commas. |
| --na_col | color | The color for NA values. |
| --cell_border_color | color | The color for the border of cells. |
| --region_info_color_list | colors | The colors for region annotations. (eg: 'chr=black,red') |
| --cluster_rows | Perform clustering on rows. | |
| --clustering_distance_rows | type | Method of measuring distance when clustring on rows, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_rows | type | Method to perform hierarchical clustering on rows, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --row_dend_side | type | The position of the row dendrogram, 'left' or 'right'. |
| --row_dend_width | numeric | The width of the row dendrogram. |
| --row_sorted | string | The sorted row names, separated by commas. It doesn't work when '--cluster_rows' is used. |
| --show_row_names | Show row names. | |
| --row_names_side | type | The position of row names, 'left' or 'right'. |
| --row_names_size | numeric | The size of row names. |
| --row_names_rot | numeric | The rotation of row names. |
| --cluster_columns | Perform clustering on columns. | |
| --clustering_distance_columns | type | Method of measuring distance when clustring on columns. choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski', 'pearson', 'spearman', 'kendall'. (Default: 'euclidean') |
| --clustering_method_columns | type | Method to perform hierarchical clustering on columns. choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --column_dend_side | type | The position of the column dendrogram, 'top' or 'bottom'. |
| --column_dend_height | numeric | The height of the column dendrogram. |
| --column_sorted | string | The sorted column names, separated by commas. It doesn't work when '--cluster_columns'. |
| --show_column_names | Show column names. | |
| --column_names_side | type | The position of column names, 'top' or 'column'. |
| --column_names_size | numeric | The size of column names. |
| --column_names_rot | numeric | The rotation of column names. |
| --anno_param_region | key=value | Parameters for the region annotation, including 'show' type ('T', 'F'), 'width' numeric, 'border' type ('T', 'F'), 'name_size' numeric, 'name_rot' numeric, 'name_side' type ('left', 'right'). |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_title | string | The text for the legend title. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| --legend_grid_size | numeric | The size of legend grid. |
| -h, --help | Print usage. | |
Usage:
apav pavPlotPhenoMan --pav <pav_file> --pheno_res <phenotype_association_result> --pheno_name <phenotype> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| --pheno | file | Phenotype file. |
| --pheno_res | file | Phenotype association result produced by command 'apav phenoStat'. |
| --pheno_name | string | Phenotype name. |
| Options: | ||
| -o, --out | string | Figure name. |
| --adjust_p | Adjust p_value. | |
| --highlight_top_n | int | The top `n` points will be highlighted. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --highlight_text_size | numeric | The size of labels on highlight points. |
| --point_size | numeric | The size of points. |
| --x_text_size | numeric | The size of tick labels on x-axis. |
| --x_text_anlge | numeric | The angle of tick labels, ranging from 0 to 1. |
| --x_title_size | numeric | The size of x-axis title. |
| --y_text_size | numeric | The size of tick labels on y-axis. |
| --y_title_size | numeric | The size of y-axis title. |
| -h, --help | Print usage. | |
Usage:
apav pavPlotPhenoBar --pav <pav_file> --pheno <phenotype_file> --region_name <region> --pheno_name <phenotype> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| --pheno | file | Phenotype file. |
| --pheno_name | string | The name of phenotype. |
| --region_name | string | The name of target region. |
| Options: | ||
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| -fig_height | numeric | The height of the figure. |
| --pav_colors | colors | The colors for presence and absence. |
| --bar_width | numeric | The relative width of bars, ranging from 0 to 1. |
| --x_text_size | numeric | The size of tick labels on x-axis. |
| --x_title_size | numeric | The size of x-axis title. |
| --y_text_size | numeric | The size of tick labels on y-axis. |
| --y_title_size | numeric | The size of y-axis title. |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| -h, --help | Print usage. | |
Usage:
apav pavPlotPhenoVio --pav <pav_file> --pheno <phenotype_file> --region_name <region> --pheno_name <phenotype> [options]
| Necessary input: | ||
| -i, --pav | file | PAV file produced by command 'apav callPAV'. |
| --pheno | file | Phenotype file. |
| --pheno_name | string | The name of phenotype. |
| --region_name | string | The name of target region. |
| Options: | ||
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --pav_colors | colors | The colors for presence and absence. |
| --x_text_size | numeric | The size of tick labels on x-axis. |
| --x_title_size | numeric | The size of x-axis title. |
| --y_text_size | numeric | The size of tick labels on y-axis. |
| --y_title_size | numeric | The size of y-axis title. |
| --legend_side | type | The position of legend, choosing from 'top', 'bottom', 'right', 'left'. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| -h, --help | Print usage. | |
Usage:
apav elePlotCov --elecov <element_coverage_file> [options]
| Necessary input: | ||
| -i, --elecov | file | Element coverage file of ONE target region. |
| Options: | ||
| --gff | file | GFF file of gene. |
| --pheno | file | Phenotype file. |
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --cluster_samples | Perform clustering on samples. | |
| --clustering_distance | type | Method to measure distance, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'. (Default: 'euclidean') |
| --cluster_method | type | Method to perform hierarchical clustering, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --ele_region | type | Element region for display, choosing from 'TN'(transcripts number), 'UP'(upstream) and 'DOWN'(downstream). |
| --top_anno_height | numeric | The relative height of annotation, ranging from 0 to 1. |
| --left_anno_width | numeric | The relative width of annotation, ranging from 0 to 1. |
| --ele_color | color | The color of element regions. |
| --ele_line_color | color | The color for the indicator line of elements. |
| --cov_colors | colors | The colors for coverage, separated by commas. |
| --gene_colors | colors | The colors for gene elements, separated by commas. The colors are assigned to 'transcript', 'exon', 'CDS', 'five_prime_UTR' and 'three_prime_UTR'. |
| --pheno_info_color_list | key=value | The colors for phenotype annotations. (eg: 'gender=blue,green') |
| --seq_name_size | numeric | The size of sequence name. |
| --loc_name_size | numeric | The size of coordinate numbers. |
| --hide_ele_name | Hide element names. | |
| --ele_name_size | numeric | The size of element names. |
| --ele_name_rot | numeric | The rotation of element names. |
| --hide_sample_name | Hide sample names. | |
| --sample_name_size | numeric | The size of sample names. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| -h, --help | Print usage page. | |
Usage:
apav elePlotPAV --elepav <element_PAV_file> [options]
| Necessary input: | ||
| -i, --elepav | file | Element PAV file of ONE target region. |
| --gff | file | GFF file of gene. |
| --pheno | file | Phenotype file. |
| -o, --out | string | Figure name. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --cluster_samples | Perform clustering on samples. | |
| --clustering_distance | type | Method to measure distance, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'. (Default: 'euclidean') |
| --cluster_method | type | Method to perform hierarchical clustering, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --ele_region | type | Gene element regions for display, choosing from 'TN'(transcripts number), 'UP'(upstream) and 'DOWN'(downstream). |
| --top_anno_height | numeric | The relative height of annotation, ranging from 0 to 1. |
| --left_anno_width | numeric | The relative width of annotation, ranging from 0 to 1. |
| --ele_color | color | The color of element regions. |
| --ele_line_color | color | The color for the indicator line of elements. |
| --pav_colors | colors | The colors for presence and absence, separated by commas. |
| --gene_colors | colors | The colors for gene elements, separated by commas. The colors are assigned to 'transcript', 'exon', 'CDS', 'five_prime_UTR' and 'three_prime_UTR'. |
| --pheno_info_color_list | key=value | The colors for phenotype annotations. (eg: 'gender=blue,green') |
| --seq_name_size | numeric | The size of sequence name. |
| --loc_name_size | numeric | The size of coordinate numbers. |
| --hide_ele_name | Hide element names. | |
| --ele_name_size | numeric | The size of element names. |
| --ele_name_rot | numeric | The rotation of element names. |
| --hide_sample_name | Hide sample names. | |
| --sample_name_size | numeric | The size of sample names. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| -h, --help | Print usage page. | |
Usage:
apav elePlotDepth --ele <element_data> --bamdir <bam_dir> [options]
| Necessary input: | ||
| -i, --ele | file | Element file. |
| -b, --bamdir | dir | The directory contains mapping results (sorted '.bam' files). |
| Options: | ||
| --gff | file | GFF file of ONE target region. |
| --pheno | file | Phenotype file. |
| -o, --out | string | Prefix of the result file. |
| Visualization options: | ||
| --fig_width | numeric | The width of the figure. |
| --fig_height | numeric | The height of the figure. |
| --cluster_samples | Perform clustering on samples. | |
| --clustering_distance | type | Method to measure distance, choosing from 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'. (Default: 'euclidean') |
| --clustering_method | type | Method to perform hierarchical clustering, choosing from 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'. (Default: 'complete') |
| --log10 | Convert depth value to log10(depth+1). | |
| --ele_region | type | Gene element regions for display, choosing from 'TN'(transcripts number), 'UP'(upstream) and 'DOWN'(downstream). |
| --top_anno_height | numeric | The relative height of annotation, ranging from 0 to 1. |
| --left_anno_width | numeric | The relative height of annotation, ranging from 0 to 1. |
| --ele_color | color | The color of element regions. |
| --depth_colors | colors | The colors of depth, separated by commas. |
| --lowlight_colors | colors | The colors for depth of non-element region, separated by commas. |
| --gene_colors | colors | The colors of gene elements, separated by commas. The colors are assigned to 'transcript', 'exon', 'CDS', 'five_prime_UTR' and 'three_prime_UTR'. |
| --pheno_info_color_list | key=value | The colors of phenotype annotations. (eg: 'gender=blue,green') |
| --seq_name_size | numeric | The size of sequence name. |
| --loc_name_size | numeric | The size of coordinate numbers. |
| --hide_sample_name | Hide sample names. | |
| --sample_name_size | numeric | The size of sample names. |
| --legend_title | numeric | The title of legend. |
| --legend_title_size | numeric | The size of legend title. |
| --legend_text_size | numeric | The size of legend item labels. |
| -h, --help | Print usage page. | |
