vDiveR (version 2.0.1)

plot_time: 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"
)

Value

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

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

Examples

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