Plot an object of class smaAgri

Create several plots for an object of class smaAgri

Usage

# S3 method for smaAgri
plot(
  x,
  type = c("summary", "correlation", "spatial"),
  filter_traits = NULL,
  nudge_y_cv = 3,
  nudge_y_h2 = 0.07,
  horizontal = FALSE,
  theme_size = 15,
  axis_size = 8,
  text_size = 4,
  ...
)

Arguments

x

An object inheriting from class smaAgri resulting of executing the function single_trial_analysis()

type

A character string specifiying the type of plot. "summary", "correlation" or "spatial".

filter_traits

An optional character vector to filter traits.

nudge_y_cv

Vertical adjustment to nudge labels by when plotting CV bars. Only works if the argument type is "summary". 3 by default.

nudge_y_h2

Vertical adjustment to nudge labels by when plotting h2 bars. Only works if the argument type is "summary". 0.07 by default.

horizontal

If FALSE, the default, the labels are plotted vertically. If TRUE, the labels are plotted horizontally.

theme_size

Base font size, given in pts. 15 by default.

axis_size

Numeric input to define the axis size.

text_size

Numeric input to define the text size.

...

Further graphical parameters. For future improvements.

Value

A ggplot object.

Author

Johan Aparicio [aut]

Examples

# \donttest{
library(agridat)
library(agriutilities)
data(besag.met)
dat <- besag.met
results <- check_design_met(
  data = dat,
  genotype = "gen",
  trial = "county",
  traits = c("yield"),
  rep = "rep",
  block = "block",
  col = "col",
  row = "row"
)
out <- single_trial_analysis(results, progress = FALSE)
print(out)
#> ---------------------------------------------------------------------
#> Summary Fitted Models:
#> ---------------------------------------------------------------------
#>     trait  trial heritability        CV    VarGen    VarErr  design
#>    <char> <char>        <num>     <num>     <num>     <num>  <char>
#> 1:  yield     C1         0.73  6.022489  87.39848  82.86095 row_col
#> 2:  yield     C2         0.37 17.104998  25.80684 108.68546 row_col
#> 3:  yield     C3         0.64 12.357202  83.57907 118.55567 row_col
#> 4:  yield     C4         0.41  8.179408  35.75568 136.21218 row_col
#> 5:  yield     C5         0.80  7.037586 103.79822  66.97523 row_col
#> 6:  yield     C6         0.49 16.632367  71.92232 207.53073 row_col
#> 
#> ---------------------------------------------------------------------
#> Outliers Removed:
#> ---------------------------------------------------------------------
#>     trait  trial genotype    id outlier
#>    <char> <fctr>   <fctr> <int>  <lgcl>
#> 1:  yield     C1      G60    50    TRUE
#> 
#> ---------------------------------------------------------------------
#> First Predicted Values and Standard Errors (BLUEs/BLUPs):
#> ---------------------------------------------------------------------
#>     trait genotype  trial    BLUEs  seBLUEs    BLUPs  seBLUPs         wt
#>    <char>   <fctr> <fctr>    <num>    <num>    <num>    <num>      <num>
#> 1:  yield      G01     C1 141.4161 6.078858 143.5308 5.249771 0.02706176
#> 2:  yield      G02     C1 157.8110 5.979708 155.8037 5.194547 0.02796663
#> 3:  yield      G03     C1 127.3836 6.091534 133.0256 5.269999 0.02694925
#> 4:  yield      G04     C1 154.8445 6.093866 153.8364 5.270427 0.02692863
#> 5:  yield      G05     C1 163.8950 6.132141 161.1831 5.271809 0.02659352
#> 6:  yield      G06     C1 128.5168 6.087902 133.6857 5.247130 0.02698141
#> 
plot(out, type = "summary", horizontal = TRUE)
#> Warning: The `facets` argument of `facet_grid()` is deprecated as of ggplot2 2.2.0.
#> ℹ Please use the `rows` argument instead.
#> ℹ The deprecated feature was likely used in the agriutilities package.
#>   Please report the issue at
#>   <https://github.com/AparicioJohan/agriutilities/issues>.

plot(out, type = "correlation")

plot(out, type = "spatial")






# }