geneBatch

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.

generalBatch

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.

gff2bed

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'


staCov

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:
  • '--rep XXX' only works with '--asgene';
  • '--merge' only works without '--rmele'


mergeElecov

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.

covPlotHeat

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


callPAV

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.

gFamPAV

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.

mergeElePAV

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.

pavSize

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.

pavPlotSize

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.

pavPlotStat

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.

pavPlotHeat

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


pavPlotBar

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.

pavPCA

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.

pavCluster

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.

pavStaPheno

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.

pavPlotPhenoHeat

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.

pavPlotPhenoBlock

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.

pavPlotPhenoMan

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.

pavPlotPhenoBar

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.

pavPlotPhenoVio

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.

elePlotCov

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.

elePlotPAV

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.

elePlotDepth

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.