add_cld {canprot}

R Documentation

Compact letter display

Description

Adds compact letter display (significant difference letters) to a boxplot.

Usage

  add_cld(datlist, bp, dx = NULL, dy = NULL)

Arguments

datlist	list, list of data values for different groups
bp	list, output of boxplot
dx	numeric, offset for letters in the x direction
dy	numeric, offset for letters in the y direction

Details

This function adds a compact letter display (cld) to an existing boxplot. It calculates a one-way ANOVA with aov followed by Tukey's Honest Significant Differences with TukeyHSD, then obtains the cld with multcompLetters4. The letters are added to the plot at the upper right sides of the bars. Default values for dx and dy are computed from the current plot dimensions; these values can be adjusted if needed.

Value

Invisibly returns a list with dx, dy, and letters (letters used for the cld, in the same order as the groups in datlist).

Examples

# Are there significant differences of nH2O among human proteins with different Zc?
aa <- get("human.aa", canprot)
# Remove extremely short sequences
aa <- aa[!plength(aa) < 20, ]
Zc <- Zc(aa)
ilo <- Zc < -0.15
ihi <- Zc > -0.10
imid <- !ilo & !ihi
nH2O <- nH2O(aa)
nH2Olist <- list(lo.Zc = nH2O[ilo], mid.Zc = nH2O[imid], hi.Zc = nH2O[ihi])
bp <- boxplot(nH2Olist, ylab = cplab$nH2O)
add_cld(nH2Olist, bp)
# Yes, higher Zc is associated with lower nH2O

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