plot.ratios: Plot heat maps with genotype ranking

Description Usage Arguments Details Author(s) Examples

Description

Plot heat maps with genotype ranking in two ways.

Usage

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## S3 method for class 'WAASBYratio'
plot(x, type, export = FALSE, file.type = "pdf",
     file.name = NULL, width = 6, height = 5, size.lab = 1,
     margins = c(5, 4),  y.lab = NULL, x.lab = NULL,
     key.lab = "Genotype ranking", resolution = 300, ...)

## S3 method for class 'WAASratio.AMMI'
plot(x, type, export = FALSE, file.type = "pdf",
     file.name = NULL, width = 6, height = 5, size.lab = 1,
     margins = c(5, 4),  y.lab = NULL, x.lab = NULL,
     key.lab = "Genotype ranking", resolution = 300, ...)

Arguments

x

The WAASYratio object

type

1 = Heat map Ranks: this graphic shows the genotype ranking considering the WAAS estimated with different numbers of Principal Components; 2 = Heat map WAASY-GY ratio: this graphic shows the genotype ranking considering the different combinations in the WAAS/GY ratio.

export

Export (or not) the plot. Default is TRUE.

file.type

If export = TRUE define the type of file to be exported. Default is pdf, Graphic can also be exported in *.tiff format by declaring file.type = "tiff".

file.name

The name of the file for exportation, default is NULL, i.e. the files are automatically named.

width

The width "inch" of the plot. Default is 8.

height

The height "inch" of the plot. Default is 7.

size.lab

The label size of the plot. It is suggested attribute 1

margins

Numeric vector of length 2 containing the margins for column and row names, respectively. Default is c(5, 4).

y.lab

The label of y axis. Default is "Genotypes".

x.lab

The label of x axis. Default is "Number of axes".

key.lab

The label of color key. Default is "Genotype ranking".

resolution

Valid parameter if file.type = "tiff". Define the resolution of the plot. Default is "300".

...

Other arguments of the function

Details

The first type of heatmap shows the genotype ranking depending on the number of principal component axis used for estimating the WAASB index. An euclidian distance-based dendrogram is used for grouping the genotype ranking for both genotypes and principal component axis. The second type of heatmap shows the genotype ranking depending on the WAASB/GY ratio. The ranks obtained with a ratio of 100/0 considers exclusively the stability for the genotype ranking. On the other hand, a ratio of 0/100 considers exclusively the productivity for the genotype ranking. Four clusters are estimated (1) unproductive and unstable genotypes; (2) productive, but unstable genotypes; (3) stable, but unproductive genotypes; and (4), productive and stable genotypes.

Author(s)

Tiago Olivoto [email protected]

Examples

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## Not run: 
library(METAAB)
wratio = WAASBYratio(data_ge,
                     resp = GY,
                     gen = GEN,
                     env = ENV,
                     rep = REP,
                     increment = 10)
plot(wratio, type = 1)

wratio2 = WAASratio.AMMI(data_ge,
                         resp = GY,
                         gen = GEN,
                         env = ENV,
                         rep = REP,
                         increment = 5)
plot(wratio2, type = 2)

## End(Not run)

TiagoOlivoto/WAASB documentation built on April 1, 2019, 10:25 a.m.