Package 'vDiveR'

k-mer sequences concatenation

Description

This function concatenates completely (index incidence = 100 index incidence < 100 k-mer position or are adjacent to each other and generate the CCS/HCS sequence in either CSv or FASTA format

Usage

concat_conserved_kmer(
  data,
  conservation_level = "HCS",
  kmer = 9,
  threshold_pct = NULL
)

Arguments

data	DiMA JSON converted csv file data
conservation_level	CCS (completely conserved) / HCS (highly conserved)
kmer	size of the k-mer window
threshold_pct	manually set threshold of index.incidence for HCS

Value

A list wit csv and fasta dataframes

Examples

csv<-concat_conserved_kmer(proteins_1host)$csv
csv_2hosts<-concat_conserved_kmer(protein_2hosts, conservation_level = "CCS")$csv
fasta <- concat_conserved_kmer(protein_2hosts, conservation_level = "HCS")$fasta

---

Extract metadata via fasta file from GISAID

Description

This function get the metadata from each header of GISAID fasta file

Usage

extract_from_GISAID(file_path)

Arguments

file_path

path of fasta file

---

Extract metadata via fasta file from ncbi

Description

This function get the metadata from each head of fasta file

Usage

extract_from_NCBI(file_path)

Arguments

file_path

path of fasta file

---

DiMA (v5.0.9) JSON Output File

Description

A sample DiMA JSON Output File which acts as the input for JSON2CSV()

Usage

JSON_sample

Format

A Diversity Motif Analyzer (DiMA) tool JSON file

---

JSON2CSV

Description

This function converts DiMA (v5.0.9) JSON output file to a dataframe with 17 predefined columns which further acts as the input for other functions provided in this vDiveR package.

Usage

json2csv(
  json_data,
  host_name = "unknown host",
  protein_name = "unknown protein"
)

Arguments

json_data	DiMA JSON output dataframe
host_name	name of the host species
protein_name	name of the protein

Value

A dataframe which acts as input for the other functions in vDiveR package

Examples

inputdf<-json2csv(JSON_sample)

---

Metadata Input Sample

Description

A dummy dataset that acts as an input for plot_world_map() and plot_time()

Usage

metadata

Format

A data frame with 1000 rows and 3 variables:

ID

unique identifier of the sequence

region

geographical region of the sequence collection

date

collection date of the sequence

---

Metadata Extraction from NCBI/GISAID (EpiFlu/EpiCoV/EpiPox/EpiArbo) FASTA file

Description

This function retrieves metadata (ID, region, date) from the input FASTA file, with the source of, either NCBI (with default FASTA header) or GISAID (with default FASTA header). The function will return a dataframe that has three columns consisting ID, collected region and collected date. Records that do not have region or date information will be excluded from the output dataframe.

Usage

metadata_extraction(file_path, source)

Arguments

file_path	path of fasta file
source	the source of fasta file, either "NCBI" or "GISAID"

Value

A dataframe that has three columns consisting ID, collected region and collected date

Examples

filepath <- system.file('extdata','GISAID_EpiCoV.faa', package = 'vDiveR')
meta_gisaid <- metadata_extraction(filepath, 'GISAID')

---

Conservation Levels Distribution Plot

Description

This function plots conservation levels distribution of k-mer positions, which consists of completely conserved (black) (index incidence = 100%), highly conserved (blue) (90% <= index incidence < 100%), mixed variable (green) (20% < index incidence <= 90%), highly diverse (purple) (10% < index incidence <= 20%) and extremely diverse (pink) (index incidence <= 10%).

Usage

plot_conservation_level(
  df,
  protein_order = NULL,
  conservation_label = 1,
  host = 1,
  base_size = 11,
  line_dot_size = 2,
  label_size = 2.6,
  alpha = 0.6
)

Arguments

df	DiMA JSON converted csv file data
protein_order	order of proteins displayed in plot
conservation_label	0 (partial; show present conservation labels only) or 1 (full; show ALL conservation labels) in plot
host	number of host (1/2)
base_size	base font size in plot
line_dot_size	lines and dots size
label_size	conservation labels font size
alpha	any number from 0 (transparent) to 1 (opaque)

Value

A plot

Examples

plot_conservation_level(proteins_1host, conservation_label = 1,alpha=0.8, base_size = 15)
plot_conservation_level(protein_2hosts, conservation_label = 0, host=2)

---

Entropy and total variant incidence correlation plot

Description

This function plots the correlation between entropy and total variant incidence of all the provided protein(s).

Usage

plot_correlation(
  df,
  host = 1,
  alpha = 1/3,
  line_dot_size = 3,
  base_size = 11,
  ylabel = "k-mer entropy (bits)\n",
  xlabel = "\nTotal variants (%)",
  ymax = ceiling(max(df$entropy)),
  ybreak = 0.5
)

Arguments

df	DiMA JSON converted csv file data
host	number of host (1/2)
alpha	any number from 0 (transparent) to 1 (opaque)
line_dot_size	dot size in scatter plot
base_size	base font size in plot
ylabel	y-axis label
xlabel	x-axis label
ymax	maximum y-axis
ybreak	y-axis breaks

Value

A scatter plot

Examples

plot_correlation(proteins_1host)
plot_correlation(protein_2hosts, base_size = 2, ybreak=1, ymax=10, host = 2)

---

Dynamics of Diversity Motifs (Protein) Plot

Description

This function compactly display the dynamics of diversity motifs (index and its variants: major, minor and unique) in the form of dot plot(s) as well as violin plots for all the provided individual protein(s).

Usage

plot_dynamics_protein(
  df,
  host = 1,
  protein_order = NULL,
  base_size = 8,
  alpha = 1/3,
  line_dot_size = 3,
  bw = "nrd0",
  adjust = 1
)

Arguments

df	DiMA JSON converted csv file data
host	number of host (1/2)
protein_order	order of proteins displayed in plot
base_size	base font size in plot
alpha	any number from 0 (transparent) to 1 (opaque)
line_dot_size	dot size in scatter plot
bw	smoothing bandwidth of violin plot (default: nrd0)
adjust	adjust the width of violin plot (default: 1)

Value

A plot

Examples

plot_dynamics_protein(proteins_1host)

---

Dynamics of Diversity Motifs (Proteome) Plot

Description

This function compactly display the dynamics of diversity motifs (index and its variants: major, minor and unique) in the form of dot plot as well as violin plot for all the provided proteins at proteome level.

Usage

plot_dynamics_proteome(
  df,
  host = 1,
  line_dot_size = 2,
  base_size = 10,
  alpha = 1/3,
  bw = "nrd0",
  adjust = 1
)

Arguments

df	DiMA JSON converted csv file data
host	number of host (1/2)
line_dot_size	size of dot in plot
base_size	word size in plot
alpha	any number from 0 (transparent) to 1 (opaque)
bw	smoothing bandwidth of violin plot (default: nrd0)
adjust	adjust the width of violin plot (default: 1)

Value

A plot

Examples

plot_dynamics_proteome(proteins_1host)

---

Entropy plot

Description

This function plot entropy (black) and total variant (red) incidence of each k-mer position across the studied proteins and highlight region(s) with zero entropy in yellow. k-mer position with low support is marked with a red triangle underneath the x-axis line.

Usage

plot_entropy(
  df,
  host = 1,
  protein_order = "",
  kmer_size = 9,
  ymax = 10,
  line_size = 2,
  base_size = 8,
  all = TRUE,
  highlight_zero_entropy = TRUE
)

Arguments

df	DiMA JSON converted csv file data
host	number of host (1/2)
protein_order	order of proteins displayed in plot
kmer_size	size of the k-mer window
ymax	maximum y-axis
line_size	size of the horizontal (reference) line in plot
base_size	word size in plot
all	plot both the entropy and total variants (pass FALSE in to plot only the entropy)
highlight_zero_entropy	highlight region with zero entropy (default: TRUE)

Value

A plot

Examples

plot_entropy(proteins_1host)
plot_entropy(protein_2hosts, host = 2)

---

Time Distribution of Sequences Plot

Description

This function plots the time distribution of provided sequences in the form of bar plot with 'Month' as x-axis and 'Number of Sequences' as y-axis. Aside from the plot, this function also returns a dataframe with 2 columns: 'Date' and 'Number of sequences'. The input dataframe of this function is obtainable from metadata_extraction(), with NCBI Protein / GISAID (EpiFlu/EpiCoV/EpiPox/EpiArbo) FASTA file as input.

Usage

plot_time(
  metadata,
  date_format = "%Y-%m-%d",
  base_size = 8,
  date_break = "2 month",
  scale = "count"
)

Arguments

metadata	a dataframe with 3 columns, 'ID', 'region', and 'date'
date_format	date format of the input dataframe
base_size	word size in plot
date_break	date break for the scale_x_date
scale	plot counts or log scale the data

Value

A single plot or a list with 2 elements (a plot followed by a dataframe, default)

Examples

time_plot <- plot_time(metadata, date_format="%d/%m/%Y")$plot
time_df <- plot_time(metadata, date_format="%d/%m/%Y")$df

---

Geographical Distribution of Sequences Plot

Description

This function plots a world map and color the affected geographical region(s) from light (lower) to dark (higher), depends on the cumulative number of sequences. Aside from the plot, this function also returns a dataframe with 2 columns: 'Region' and 'Number of Sequences'. The input dataframe of this function is obtainable from metadata_extraction(), with NCBI Protein / GISAID (EpiFlu/EpiCoV/EpiPox/EpiArbo) FASTA file as input.

Usage

plot_world_map(metadata, base_size = 8)

Arguments

metadata	a dataframe with 3 columns, 'ID', 'region', and 'date'
base_size	word size in plot

Value

A list with 2 elements (a plot followed by a dataframe)

Examples

geographical_plot <- plot_world_map(metadata)$plot
geographical_df <- plot_world_map(metadata)$df

---

DiMA (v5.0.9) JSON converted-CSV Output Sample 2

Description

A dummy dataset with 1 protein (Core) from two hosts, human and bat

Usage

protein_2hosts

Format

A data frame with 200 rows and 17 variables:

proteinName

name of the protein

position

starting position of the aligned, overlapping k-mer window

count

number of k-mer sequences at the given position

lowSupport

k-mer position with sequences lesser than the minimum support threshold (TRUE) are considered of low support, in terms of sample size

entropy

level of variability at the k-mer position, with zero representing completely conserved

indexSequence

the predominant sequence (index motif) at the given k-mer position

index.incidence

the fraction (in percentage) of the index sequences at the k-mer position

major.incidence

the fraction (in percentage) of the major sequence (the predominant variant to the index) at the k-mer position

minor.incidence

the fraction (in percentage) of minor sequences (of frequency lesser than the major variant, but not singletons) at the k-mer position

unique.incidence

the fraction (in percentage) of unique sequences (singletons, observed only once) at the k-mer position

totalVariants.incidence

the fraction (in percentage) of sequences at the k-mer position that are variants to the index (includes: major, minor and unique variants)

distinctVariant.incidence

incidence of the distinct k-mer peptides at the k-mer position

multiIndex

presence of more than one index sequence of equal incidence

host

species name of the organism host to the virus

highestEntropy.position

k-mer position that has the highest entropy value

highestEntropy

highest entropy values observed in the studied protein

averageEntropy

average entropy values across all the k-mer positions

---

DiMA (v5.0.9) JSON converted-CSV Output Sample 1

Description

A dummy dataset with two proteins (A and B) from one host, human

Usage

proteins_1host

Format

A data frame with 806 rows and 17 variables:

proteinName

name of the protein

position

starting position of the aligned, overlapping k-mer window

count

number of k-mer sequences at the given position

lowSupport

k-mer position with sequences lesser than the minimum support threshold (TRUE) are considered of low support, in terms of sample size

entropy

level of variability at the k-mer position, with zero representing completely conserved

indexSequence

the predominant sequence (index motif) at the given k-mer position

index.incidence

the fraction (in percentage) of the index sequences at the k-mer position

major.incidence

the fraction (in percentage) of the major sequence (the predominant variant to the index) at the k-mer position

minor.incidence

the fraction (in percentage) of minor sequences (of frequency lesser than the major variant, but not singletons) at the k-mer position

unique.incidence

the fraction (in percentage) of unique sequences (singletons, observed only once) at the k-mer position

totalVariants.incidence

the fraction (in percentage) of sequences at the k-mer position that are variants to the index (includes: major, minor and unique variants)

distinctVariant.incidence

incidence of the distinct k-mer peptides at the k-mer position

multiIndex

presence of more than one index sequence of equal incidence

host

species name of the organism host to the virus

highestEntropy.position

k-mer position that has the highest entropy value

highestEntropy

highest entropy values observed in the studied protein

averageEntropy

average entropy values across all the k-mer positions

---