VhgTabularRasa: VhgTabularRasa: Generate Custom Formatted Graphical Tables

Description

VhgTabularRasa creates a formatted table using the gt package.

Usage

VhgTabularRasa(
  file,
  title = "Graphical Table",
  title_align = "left",
  names_ = NULL,
  align = "left",
  subtitle = NULL,
  data_row.pad = 6,
  column_colour = "dodgerblue4",
  title_size = 26,
  subtitle_size = 14,
  title_weight = "bold",
  title_colour = "dodgerblue4",
  table_font_size = 14,
  cell_colour = "grey90",
  col_everyrow = FALSE
)

Value

Returns a gt table object formatted according to the specified parameters.

Arguments

file: A data frame.
title: (optional): The title of the plot (default: "Graphical Table").
title_align: (optional): A character vector specifying the alignment of title (and subtitle) text. Possible values are "left" (default), "center", or "right".
names_: (optional): A vector containing column names, with a length matching the number of columns in the file argument (default: names(file)).
align: (optional): A character vector specifying the alignment of text in the table columns. Possible values are "left" (default), "center", or "right".
subtitle: (optional): A character specifying the subtitle of the plot (default: NULL).
data_row.pad: (optional): Numeric value specifying the row padding (default: 6).
column_colour: (optional): character specifying the background colour for the column header (default: "dodgerblue4").
title_size: (optional): The size of the title text (default: 26).
subtitle_size: (optional): Numeric specifying the size of the subtitle text (default: 14).
title_weight: (optional): Character or numeric value specifying title font weight. The weight of the font can be modified thorough a text-based option such as "normal", "bold" (default), "lighter", "bolder", or, a numeric value between 1 and 1000, inclusive.
title_colour: (optional): A character specifying the color for the title text (default: "dodgerblue4").
table_font_size: (optional): Numeric value specifying table font size. This will change font size for the column header and for all values in each cell (default: 14).
cell_colour: (optional): Character specifying cell colour (default: "grey90").
col_everyrow: (optional): Bool value specifying if every row or every second row of the table should be filled with the colour from the cell_colour argument. col_everyrow = TRUE colors every row and col_everyrow = FALSE (default) colors every second row.

Author

Sergej Ruff

Details

VhgTabularRasa creates a formatted table using the gt package, based on input data with specified column names. It is particularly useful for generating tables that cannot be produced with vhRunsTable, when the input data does not originate from the vhRunsBarplot functions.

The VhgTabularRasa function allows users to generate tables styled like Virusparies tables using their own input data. Additionally, users can create custom tables by adjusting the parameters within this function.

VhgTabularRasa just like vhRunsTable empowers users to tailor their tables to suit their needs. With its customizable features, users can effortlessly modify titles, subtitles, and column names. By default, column names are derived from the data frame's structure using names(file). If the data frame lacks column names, an error message is triggered. However, users can supply their own column names via the names_ argument, requiring a vector of names matching the data frame's column count.

VhgTabularRasa takes data frames as Input. Passing any other object type results in an error message. Users can fine-tune their tables with options to adjust text attributes, alignment, and size, as well as row padding and color schemes for titles, subtitles, columns, and backgrounds. If that is not enough, VhgTabularRasa returns an gt tables object, which can be further manipulated with the gt package available on CRAN.

References

Iannone R, Cheng J, Schloerke B, Hughes E, Lauer A, Seo J(2024). gt: Easily Create Presentation-Ready DisplayTables. R package version 0.10.1,https://CRAN.R-project.org/package=gt.

Examples

Run this code

path <- system.file("extdata", "virushunter.tsv", package = "Virusparies")
vh_file <- ImportVirusTable(path)

# plot 1: plot boxplot for "identity"
identity <- VhgBoxplot(vh_file,y_column = "ViralRefSeq_ident")

# generate table
VhgTabularRasa(identity$summary_stats)


# example 2: plot part of Vh_file (could be any other table)
# using first 10 rows of SRA_run,num_hits,bestquery,ViralRefSeq_E and Identity col.
vh_file_part <- vh_file[c(1:10),c(1,7,9,10,11)]

VhgTabularRasa(vh_file_part,title = "first 10 rows of vh_file",subtitle =
"example for any table",names_ = c("Runs","Number of Contigs","Best Query Result",
"Refrence E-Value","Refrence Identity"))

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