Frequency Distribution Histogram

Source: R/freqdist.evaluate.core.R

Plot stacked frequency distribution histogram to graphically compare the probability distributions of traits between entire collection (EC) and core set (CS).

freqdist.evaluate.core(
  data,
  names,
  quantitative,
  qualitative,
  selected,
  highlight = NULL,
  include.highlight = TRUE,
  highlight.se = NULL,
  highlight.col = "red"
)

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.

quantitative

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

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.

highlight

Individual names to be highlighted as a character vector.

include.highlight

If TRUE, the highlighted individuals are included in the frequency distribution histogram. Default is TRUE.

highlight.se

Optional data frame of standard errors for the individuals specified in highlight. It should have the same column names as in data.

highlight.col

The colour(s) to be used to highlighting individuals in the plot as a character vector of the same length as highlight. Must be valid colour values in R (named colours, hexadecimal representation, index of colours [1:8] in default R palette() etc.).

Value

A list with the ggplot objects of stacked frequency distribution histograms plots for each trait specified as quantitative and qualitative.

See also

hist, geom_histogram

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)))

# \donttest{
freqdist.evaluate.core(data = ec, names = "genotypes",
                       quantitative = quant, qualitative = qual,
                       selected = core)
#> $NMSR

#> 
#> $TTRN

#> 
#> $TFWSR

#> 
#> $TTRW

#> 
#> $TFWSS

#> 
#> $TTSW

#> 
#> $TTPW

#> 
#> $AVPW

#> 
#> $ARSR

#> 
#> $SRDM

#> 
#> $CUAL

#> 
#> $LNGS

#> 
#> $PTLC

#> 
#> $DSTA

#> 
#> $LFRT

#> 
#> $LBTEF

#> 
#> $CBTR

#> 
#> $NMLB

#> 
#> $ANGB

#> 
#> $CUAL9M

#> 
#> $LVC9M

#> 
#> $TNPR9M

#> 
#> $PL9M

#> 
#> $STRP

#> 
#> $STRC

#> 
#> $PSTR

#> 

checks <- c("TMe-1199", "TMe-1957", "TMe-3596", "TMe-3392")

freqdist.evaluate.core(data = ec, names = "genotypes",
                       quantitative = quant, qualitative = qual,
                       selected = core,
                       highlight = checks, highlight.col = "red")


























#> $NMSR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTRN
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TFWSR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTRW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TFWSS
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTSW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTPW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $AVPW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $ARSR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $SRDM
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $CUAL
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $LNGS
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $PTLC
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $DSTA
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $LFRT
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $LBTEF
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $CBTR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $NMLB
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $ANGB
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $CUAL9M
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $LVC9M
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TNPR9M
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $PL9M
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $STRP
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $STRC
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $PSTR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 

quant.se <- data.frame(genotypes = checks,
                       NMSR = c(0.107, 0.099, 0.106, 0.062),
                       TTRN = c(0.081, 0.072, 0.057, 0.049),
                       TFWSR = c(0.089, 0.031, 0.092, 0.097),
                       TTRW = c(0.064, 0.031, 0.071, 0.071),
                       TFWSS = c(0.106, 0.071, 0.121, 0.066),
                       TTSW = c(0.084, 0.045, 0.066, 0.054),
                       TTPW = c(0.098, 0.052, 0.111, 0.082),
                       AVPW = c(0.074, 0.038, 0.054, 0.061),
                       ARSR = c(0.104, 0.019, 0.204, 0.044),
                       SRDM = c(0.078, 0.138, 0.076, 0.079))

freqdist.evaluate.core(data = ec, names = "genotypes",
                       quantitative = quant,
                       selected = core,
                       highlight = checks, highlight.col = "red",
                       highlight.se = quant.se)










#> $NMSR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTRN
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TFWSR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTRW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TFWSS
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTSW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $TTPW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $AVPW
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $ARSR
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
#> $SRDM
#> TableGrob (1 x 2) "arrange": 2 grobs
#>   z     cells    name              grob
#> 1 1 (1-1,1-1) arrange    gtable[layout]
#> 2 2 (1-1,2-2) arrange gtable[guide-box]
#> 
# }