Bar Plots

Plot Bar plots to graphically compare the frequency distributions of qualitative traits between entire collection (EC) and core set (CS).

bar.evaluate.core(data, names, qualitative, selected)

Arguments

data

The data as a data frame object. The data frame should possess one row per individual and columns with the individual names and multiple trait/character data.

names

Name of column with the individual names as a character string.

qualitative

Name of columns with the qualitative traits as a character vector.

selected

Character vector with the names of individuals selected in core collection and present in the names column.

Value

A list with the ggplot objects of relative frequency bar plots of CS and EC for each trait specified as qualitative.

See also

barplot, geom_bar

Examples

data("cassava_CC")
data("cassava_EC")

ec <- cbind(genotypes = rownames(cassava_EC), cassava_EC)
ec$genotypes <- as.character(ec$genotypes)
rownames(ec) <- NULL

core <- rownames(cassava_CC)

quant <- c("NMSR", "TTRN", "TFWSR", "TTRW", "TFWSS", "TTSW", "TTPW", "AVPW",
           "ARSR", "SRDM")
qual <- c("CUAL", "LNGS", "PTLC", "DSTA", "LFRT", "LBTEF", "CBTR", "NMLB",
          "ANGB", "CUAL9M", "LVC9M", "TNPR9M", "PL9M", "STRP", "STRC",
          "PSTR")

ec[, qual] <- lapply(ec[, qual],
                     function(x) factor(as.factor(x)))

bar.evaluate.core(data = ec, names = "genotypes",
                  qualitative = qual, selected = core)
#> $CUAL
#> Warning: The dot-dot notation (`..prop..`) was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(prop)` instead.
#> ℹ The deprecated feature was likely used in the EvaluateCore package.
#>   Please report the issue at
#>   <https://github.com/aravind-j/EvaluateCore/issues>.

#> 
#> $LNGS

#> 
#> $PTLC

#> 
#> $DSTA

#> 
#> $LFRT

#> 
#> $LBTEF

#> 
#> $CBTR

#> 
#> $NMLB

#> 
#> $ANGB

#> 
#> $CUAL9M

#> 
#> $LVC9M

#> 
#> $TNPR9M

#> 
#> $PL9M

#> 
#> $STRP

#> 
#> $STRC

#> 
#> $PSTR

#>