pretty_pvalues: Round and format a vector of p-values

In FredHutch/VISCfunctions: VISC STP/SRA functions

Round and format a vector of p-values

Description

pretty_pvalues() takes a vector of p-values, rounds them to a specified digit amount, allows options for emphasizing p-values < the defined significance level, and returns a character for missing.

Usage

pretty_pvalues(
  pvalues,
  digits = 3,
  bold = FALSE,
  italic = FALSE,
  background = NULL,
  sig_alpha = 0.05,
  missing_char = "---",
  include_p = FALSE,
  trailing_zeros = TRUE,
  output_type = c("latex", "html", "pandoc", "no_markup")
)

Arguments

pvalues	numeric vector of raw p-values to be formatted
digits	number of digits to round to; values with zeros past this number of digits are truncated
bold	TRUE or FALSE: set to TRUE to bold p-values < the defined significance level
italic	TRUE or FALSE: set to TRUE to italicize p-values < the defined significance level
background	highlight color for p-values < the defined significance level. Default = NULL (no highlighting)
sig_alpha	the defined significance level. Default = 0.05
missing_char	character string that will replace missing values from the p-value vector. Default = "—"
include_p	TRUE or FALSE: set to TRUE to print "p = " before each p-value
trailing_zeros	TRUE or FALSE: default = TRUE, p-values are formatted with trailing zeros to the defined number of digits (i.e. 0.100 instead of 0.1 if digits = 3)
output_type	output type, "latex" (default), "html" , "pandoc" (for Word document output), or "no_markup"

Details

With this function, there are two things to be noted: Since the p-value vector formatting uses cell_spec, which generates raw HTML or LaTeX, or uses custom markdown syntax for the pandoc option, make sure you remember to put escape = FALSE into your kable code when generating your table. At the same time, you will need to escape special symbols manually. Additionally, cell_spec needs a way to know whether you want HTML, LaTeX, or Markdown (pandoc) output. You can specify it locally in the function or globally using options(knitr.table.format = "latex"). If you don't provide anything, this function will output as HTML by default.

For pandoc markup only bold and italic can be specified. Both can jointly be specified for bold italics.

Value

Vector of transformed p-values for table output

Examples

pvalue_example = c(1, 0.06, 0.0005, NA, 1e-6)

pretty_pvalues(pvalue_example, background = "pink")

pretty_pvalues(pvalue_example, digits = 4, missing_char = "missing",
               bold = TRUE)

# How to use pretty_pvalues in reports
raw_pvals <- c(0.00000007, .05000001, NaN, NA, 0.783)
pretty_pvals <- pretty_pvalues(raw_pvals , digits = 3, background = "green",
                               italic = TRUE, bold = TRUE)
kableExtra::kable(pretty_pvals , format = "latex", escape = FALSE,
                  col.names = c("P-values"))

FredHutch/VISCfunctions documentation built on Oct. 14, 2024, 11:33 p.m.