format_table_simple: Format a table rather simply to look nice in a Word file

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

Format a table rather simply to look nice in a Word file

Description

format_table_simple is meant to for use with writing compound summary files. It is a wrapper function for formatTable_Simcyp that creates a somewhat simpler style of table.

Usage

format_table_simple(
  DF,
  shading_column,
  merge_shaded_cells = TRUE,
  merge_columns = NA,
  sort_column,
  bold_cells = list(c(0, NA)),
  highlight_gmr_colors = NA,
  highlight_so_cutoffs = NA,
  highlight_so_colors = "yellow to red",
  font = "Palatino Linotype",
  fontsize = 11,
  column_widths = NA,
  include_header = TRUE,
  alignment = "left",
  save_table = NA,
  page_orientation = "portrait",
  title_document = NA,
  table_caption = NA
)

Arguments

DF	a data.frame
shading_column	If you would like to alternate the shading of the rows in the output table, supply here the unquoted name of the column to check for when to change the shading; every time that column's value changes, the shading will alternate between white and light gray. For example, if you have a table with PK values for multiple files and you have more than one row per file (an example of this would be the output from the function pksummary_mult), setting shading_column = File will cause the shading of the rows to alternate between white and light gray whenever the file changes. Please see the examples at the bottom of this help file.
merge_shaded_cells	TRUE (default) or FALSE for whether to merge the cells that have the same shade. This only applies when one of the columns in the input data.frame is used for deciding when to alternate shading, that is, shading_column has a value.
merge_columns	a vector of quoted column names or of numeric column positions that should be merged vertically whenever the values are the same. For example, merge_columns = c("File", "Tissue") will cause the cells in the columns "File" and "Tissue" to merge vertically whenever the same value shows up in consecutive rows. Similarly, merge_columns = c(1, 3, 5) will merge vertically the 1st, 3rd, and 5th columns whenever the values are the same. Note: This is different from most other functions in the SimcypConsultancy package, which require unquoted column names. Honestly, we just don't know how code things for you to supply a variable number of unquoted column names for a single argument; we've just hit a coding knowledge limitation here!
bold_cells	optionally specify cells in the table to be in bold-face text with a numeric vector where the 1st number is the row number and the 2nd number is the column number (just like regular row and column specifications in R). For example, bold_cells = c(1, 2) will make the cell in row 1 and column 2 bold face. Use "0" for the row number if you want to use bold face for something in the header row, and use NA in place of a row or column number to make everything in that row or column bold face. If you want to specify multiple places to use bold face, use a list of numeric vectors. By default, the header row will be bold. Set bold_cells = NA to make nothing bold. Please see the examples at the bottom of the help file.
highlight_gmr_colors	optionally specify a set of colors to use for highlighting geometric mean ratios for DDIs. Options are "yellow to red", "green to red", "traffic" (a more vivid version of "green to red"), or a vector of 4 colors of your choosing. If left as NA, no highlighting for GMR level will be done.
highlight_so_cutoffs	optionally specify cutoffs for highlighting any simulated-to-observed ratios. Anything that is above those values or below the inverse of those values will be highlighted. To figure out what cells to highlight, this looks for a column titled "Statistic" or "Stat", then looks for what row contains "S/O" or "simulated (something something) observed" (as in, we'll use some wildcards to try to match your specific text). Next, it looks for any values in that same row that are above those cutoffs. This overrides anything else you specified for highlighting. The default is NA, for not highlighting based on S/O value. Acceptable input for, say, highlighting values that are > 125% or < 80% of the observed and also, with a second color, values that are > 150% or < 66% would be: highlight_so_cutoffs = c(1.25, 1.5). If you would like the middle range of values to be highlighted, include 1 in your cutoffs. For example, say you would like everything that's < 80% or > 125% to be highlighted red but you'd like the "good" values from 80% to 125% to be green, you can get that by specifying highlight_so_cutoffs = c(1, 1.25) and highlight_so_colors = c("green", "red")
highlight_so_colors	optionally specify a set of colors to use for highlighting S/O values outside the limits you specified with highlight_so_cutoffs. Options: "yellow to red" (default) A range of light yellow to light orange to light red. If you have included 1 in your cutoffs and you leave highlight_so_colors with the default setting, values in the middle, "good" range of S/O values will be highlighted a light green. "traffic" light green, yellow, and red designed to display values outside 1.25, 1.5, and 2 fold of unity, respectively. If you include 1 in highlight_so_cutoffs, you'll get a darker green for "good" S/O values. This color scheme was borrowed from Lisa, so if you've seen her slides, these will look familiar. a character vector of specific colors Any R-acceptable colors, will work here, e.g., highlight_so_colors = c("yellow", "orange", "red") . If you do specify your own bespoke colors, you'll need to make sure that you supply one color for every value in highlight_so_cutoffs.
font	font to use. Default is "Palatino Linotype" and any fonts available on your machine in either Word or PowerPoint should be acceptable. If you get Times New Roman in your table when you asked for something else, it means that that font isn't available or maybe wasn't spelled the way R is expecting it. For example, "Calibri" works but "Calibri (Body)" doesn't even though the latter is listed in PowerPoint and Word.
fontsize	the numeric font size for the output table. Default is 11 point.
column_widths	optionally specify what the widths of the columns should be with a numeric vector of the widths in inches, e.g., column_widths = c(1.5, 2, 0.5, 3)
include_header	TRUE (default) or FALSE for whether to include the header row
alignment	alignment of text throughout table. Options are "left" (default), "right", "center", or "justify".
save_table	optionally save the output table by supplying a file name in quotes here, e.g., "My nicely formatted table.docx". Do not include any slashes, dollar signs, or periods in the file name. If you leave off the file extension, we'll assume you want it to be ".docx". If there is a column titled "File" in your table, we'll add a caption listing which files were included.
page_orientation	set the page orientation for the Word file output to "portrait" (default) or "landscape"
title_document	optionally specify a title for the Word document output. If you don't save the table, this will be ignored.
table_caption	optionally add some text for a table caption. If the table you supply contains a column titled "File", there will already be a caption listing the source files; this would add some additional text before that.

Value

a formatted table

Examples

# None yet

shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.