alignment_quality_stats_plotter: Quality check graphics for DNA Barcodes

In carvajalc/BarcoR: Quality Check Graphics for DNA Barcodes

Description

Performs quality plots and quality stats

Usage

alignment_quality_stats_plotter(
  metadata_file_name_value,
  ambiguity_file_name_value,
  codons_file_name_value,
  gaps_file_name_value,
  quality_file_name_value,
  common_variable_name_meger_value,
  stripplot_quality_var_names_value,
  stripplot_group_var_names_value = "GLOBAL",
  stripplot_indicator_var_names_value,
  stripplot_mono_color_value = "gray27",
  stripplot_color_gradient_names_value = NULL,
  stripplot_color_median_value = "red",
  stripplot_alpha_value = 0.6,
  stripplot_location_n_value = 10,
  stripplot_pdf_width_height_value = c(7, 5),
  global_time_series_var_x_names_value,
  global_time_series_var_y_con_names_value,
  global_time_series_var_y_dis_names_value = NULL,
  global_plot_time_series_x_var_name,
  global_plot_time_series_group_var_name = NULL,
  global_plot_time_series_ggsci_or_user_color_names_value = c("#999999", "#E69F00",
    "#56B4E9"),
  global_plot_pdf_width_height_value = c(7, 5),
  global_plot_time_series_alpha_value = 0.6,
  per_site_plot_var_y_names_value,
  per_site_transform_gap_count_value = "sqrt",
  per_site_transform_codon_count_value = "sqrt",
  per_site_transform_ambiguity_count_value = NULL,
  per_site_plot_color_gap_names_value = c("viridis", "A"),
  per_site_plot_color_codon_names_value = c("viridis", "C"),
  per_site_plot_color_ambiguity_names_value = c("white", "blue", "red"),
  per_site_add_label_every_n_position_value = 250,
  per_site_NA_color_value = "white",
  per_site_plot_alpha_value = 1,
  per_site_plot_pdf_width_height_value = c(7, 5),
  file_out_user = NULL,
  out_directory_user = NULL
)

Arguments

metadata_file_name_value	a data frame of metadata from DNA barcodes (year, sequencing technology).
ambiguity_file_name_value	a data frame of ambiguity of DNA barcodes (see aligned_sequence_matrix_characterizer output)
codons_file_name_value	a data frame of codons of DNA barcodes (see aligned_sequence_matrix_characterizer output)
gaps_file_name_value	a data frame of gaps of DNA barcodes (see aligned_sequence_matrix_characterizer output)
quality_file_name_value	a data frame of quality of DNA barcodes (see aligned_sequence_matrix_characterizer output)
common_variable_name_meger_value	Character. Column name used to merge the metadata, ambiguity, codons, gaps and quality matrices.
stripplot_quality_var_names_value	List. Column names to be included in stripplot (see quality file for complete list of column names)
stripplot_group_var_names_value	Character. plot the whole variable ("GLOBAL") or split for technology ("technology") in violin plot
stripplot_indicator_var_names_value	Character. variables to be included in a subset from the quality file ("one_seq_ID", "Date_submission_NCBI")
stripplot_mono_color_value	points color in the stripplot.
stripplot_color_gradient_names_value	vector. colors option to be used in a gradient stripplot example ("green","black")
stripplot_color_median_value	Color option for th median value point in the stripplot
stripplot_alpha_value	numeric. Alpha value for the stripplot (see ggplot2 options)
stripplot_location_n_value	Numeric. position in y-axis of number of sequence (n) per technology.
stripplot_pdf_width_height_value	Vector. the width and height for output graphic in pdf format.
global_time_series_var_x_names_value	Vector.Variable (year) to be included in a times-series plot as x-axis. Additionally, a category can be included to group the data.
global_time_series_var_y_con_names_value	Vector. Variables to be included in a time-series plot as y-axis
global_time_series_var_y_dis_names_value	Character. a criterion for grouping sequence under same condition example: "technology"
global_plot_time_series_x_var_name	character. Variable to be included in time series analysis
global_plot_time_series_group_var_name	character. variable name to group under same color in the plot.
global_plot_time_series_ggsci_or_user_color_names_value	Vector. Color used for colorRampPalette.
global_plot_pdf_width_height_value	Vector. the width and height for output graphic in pdf format.
global_plot_time_series_alpha_value	numeric. Alpha value for the time-series (see ggplot2 options)
per_site_plot_var_y_names_value	option ("Date_submission_NCBI", "technology")
per_site_transform_gap_count_value	transformation of count gap value. Example: "sqrt"
per_site_transform_codon_count_value	transformation of count codon value. Example: "sqrt"
per_site_transform_ambiguity_count_value	transformation of count ambiguity value. Example: "sqrt"
per_site_plot_color_gap_names_value	Color option for count gaps plot.
per_site_plot_color_codon_names_value	Color option for count codon plot.
per_site_plot_color_ambiguity_names_value	Color option for count ambiguity plot.
per_site_add_label_every_n_position_value	numeric. break value in the plot.
per_site_NA_color_value	character. Color for NA values
per_site_plot_alpha_value	numeric. Alpha value for the time-series (see ggplot2 options)
per_site_plot_pdf_width_height_value	Vector. the width and height for output graphic in pdf format.
file_out_user	optional prefix name for output files
out_directory_user	output directory path

Value

A serie of graphics and files with quality stats

Examples

{
COX1_ver_1 <- alignment_quality_stats_plotter (metadata_file_name_value =
system.file("extdata","COI_UVI_seq_metadata.txt",package="BarcoR"),
ambiguity_file_name_value = system.file("extdata","COI_UVI_ambiguity_df.txt",
package="BarcoR"),
codons_file_name_value =
system.file("extdata","COI_UVI_codons_df.txt",package="BarcoR"),
gaps_file_name_value = system.file("extdata","COI_UVI_gaps_df.txt",package="BarcoR"),
quality_file_name_value = system.file("extdata","COI_UVI_quality.txt",package="BarcoR"),
common_variable_name_meger_value = "one_seq_ID",
stripplot_quality_var_names_value = c("nucleotide_adj_lenght_seq_consensus_NO_gap_percent_distance_per_total_length", "aminoacid_adj_lenght_seq_consensus_NO_gap_percent_distance_per_total_length", "namb_percent_per_total_length"),
stripplot_group_var_names_value = c("GLOBAL", "technology"),
stripplot_indicator_var_names_value = c("one_seq_ID", "Date_submission_NCBI"),
stripplot_mono_color_value = "gray25",
stripplot_color_gradient_names_value = NULL,
stripplot_color_median_value = "red",
stripplot_alpha_value = 0.6,
stripplot_location_n_value = 10,
stripplot_pdf_width_height_value = c(7,5),
global_time_series_var_x_names_value = c("Date_submission_NCBI", "technology"),
global_time_series_var_y_con_names_value = c("nsites_no_gap","nsites_amb","nimcomplete_codons","ncodons_no_X"),
global_time_series_var_y_dis_names_value = NULL,
global_plot_time_series_x_var_name = "Date_submission_NCBI",
global_plot_time_series_group_var_name = "technology",
global_plot_time_series_ggsci_or_user_color_names_value = c("#41B15A", "#289DAE", "#FB1F15"),
global_plot_time_series_alpha_value = 0.6,
global_plot_pdf_width_height_value = c(9,5),
per_site_plot_var_y_names_value = c("Date_submission_NCBI", "technology"),
per_site_transform_gap_count_value = "sqrt",
per_site_transform_codon_count_value = "sqrt",
per_site_transform_ambiguity_count_value = NULL,
per_site_plot_color_gap_names_value = c("viridis", "A"),
per_site_plot_color_codon_names_value = c("viridis", "C"),
per_site_plot_color_ambiguity_names_value = c("white","blue","red"),
per_site_add_label_every_n_position_value = 250,
per_site_NA_color_value = "gray25",
per_site_plot_alpha_value = 1,
per_site_plot_pdf_width_height_value = c(9,5),
file_out_user = "COX1_ver1",
out_directory_user = NULL)
}

carvajalc/BarcoR documentation built on Dec. 19, 2021, 1:54 p.m.