bv.development.box: Development of genetic/breeding value using a boxplot

In MoBPS: Modular Breeding Program Simulator

Description

Function to plot genetic/breeding values for multiple generation/cohorts using box plots

Usage

bv.development.box(
  population,
  database = NULL,
  gen = NULL,
  cohorts = NULL,
  bvrow = "all",
  json = FALSE,
  display = "bv",
  display.selection = FALSE,
  display.reproduction = FALSE,
  ylim = NULL,
  fix_mfrow = FALSE
)

Arguments

population	population list
database	Groups of individuals to consider for the export
gen	Quick-insert for database (vector of all generations to export)
cohorts	Quick-insert for database (vector of names of cohorts to export)
bvrow	Which traits to display (for multiple traits separte plots (par(mfrow)))
json	If TRUE extract which cohorts to plot according to the json-file used in json.simulation
display	Choose between "bv", "pheno", "bve" (default: "bv")
display.selection	Display lines between generated cohorts via selection (webinterface)
display.reproduction	Display lines between generated cohorts via reproduction (webinterface)
ylim	Set this to fix the y-axis of the plot
fix_mfrow	Set TRUE to not use mfrow - use for custom plots

Value

Genomic values of selected gen/database/cohort

Examples

data(ex_pop)
bv.development.box(ex_pop, gen=1:5)

Example output

#############################################################
############ Modular Breeding Program Simulator #############
#############################################################
################ Version: 1.4.87 (27-03-2020) ###############
######## To update to the most recent stable version: #######
## devtools::install_github('tpook92/MoBPS', subdir='pkg') ##
#############################################################
################ Web-interface: www.mobps.de ################
### Extended documentation: www.github.com/tpook92/MoBPS ####
#############################################################
$`Generation 1`
            M1_1     M2_1     M3_1     M4_1     M5_1     M6_1     M7_1     M8_1
Trait 1 98.77562 98.90339 99.50298 99.37521 101.8188 100.9908 98.77562 100.1236
            M9_1    M10_1    M11_1    M12_1    M13_1    M14_1    M15_1    M16_1
Trait 1 98.33152 101.5665 98.75559 99.29291 101.1647 100.6609 101.0582 99.48035
           M17_1    M18_1    M19_1    M20_1    M21_1    M22_1    M23_1    M24_1
Trait 1 100.4041 97.87265 100.0413 98.90151 100.6561 100.1388 98.67811 100.5331
          M25_1     F1_1    F2_1     F3_1     F4_1     F5_1     F6_1     F7_1
Trait 1 99.8874 98.41664 97.7119 98.84881 100.3986 98.67876 100.8355 99.42978
            F8_1     F9_1    F10_1    F11_1    F12_1    F13_1    F14_1    F15_1
Trait 1 100.2717 97.67418 100.4041 97.48861 99.10378 95.37697 99.24066 98.17434
           F16_1   F17_1    F18_1    F19_1   F20_1    F21_1   F22_1    F23_1
Trait 1 101.8737 99.5972 99.48035 102.6102 97.9329 98.70159 102.231 96.40713
           F24_1    F25_1
Trait 1 99.37521 98.51414

$`Generation 2`
            M1_2     M2_2    M3_2     M4_2     M5_2    M6_2     M7_2     M8_2
Trait 1 100.2075 100.3912 99.5011 102.9893 102.2755 99.9003 100.5137 98.45742
            M9_2    M10_2   M11_2    M12_2    M13_2   M14_2    M15_2    M16_2
Trait 1 100.4085 102.5998 100.863 100.0067 99.15835 102.473 101.9741 99.09026
          M17_2    M18_2    M19_2    M20_2    M21_2    M22_2   M23_2    M24_2
Trait 1 100.892 103.0543 100.1345 100.1782 102.1064 101.9741 101.097 99.46943
           M25_2     F1_2     F2_2     F3_2     F4_2     F5_2     F6_2     F7_2
Trait 1 100.9123 101.0504 103.5113 99.09806 100.3262 102.2162 103.1139 101.4865
          F8_2     F9_2    F10_2    F11_2    F12_2    F13_2    F14_2    F15_2
Trait 1 100.83 99.82248 101.8269 103.5167 99.74442 102.3258 99.73532 98.52682
           F16_2    F17_2    F18_2    F19_2    F20_2    F21_2   F22_2    F23_2
Trait 1 100.6835 101.1873 101.8188 101.1647 98.15171 100.6383 102.473 100.5331
           F24_2    F25_2
Trait 1 100.2482 102.2084

$`Generation 3`
            M1_3     M2_3     M3_3     M4_3     M5_3     M6_3     M7_3     M8_3
Trait 1 101.8188 102.8852 101.4293 103.3889 101.7046 102.3258 102.6102 101.3151
            M9_3    M10_3    M11_3   M12_3    M13_3   M14_3    M15_3    M16_3
Trait 1 102.8522 101.1647 103.2314 101.956 100.0067 102.198 103.1171 101.6989
           M17_3    M18_3    M19_3    M20_3   M21_3    M22_3    M23_3    M24_3
Trait 1 101.4478 102.8522 102.1487 102.3588 102.198 103.1171 102.8522 102.8522
           M25_3     F1_3    F2_3     F3_3    F4_3     F5_3     F6_3     F7_3
Trait 1 101.7046 103.3889 102.618 102.6102 102.231 103.3889 103.5113 102.0734
            F8_3     F9_3    F10_3    F11_3    F12_3    F13_3    F14_3    F15_3
Trait 1 104.0431 103.5294 101.9466 101.5768 102.0884 103.2495 102.0702 100.9305
           F16_3    F17_3    F18_3    F19_3    F20_3    F21_3    F22_3    F23_3
Trait 1 102.0734 102.6102 103.3889 101.0582 104.4223 101.4296 102.2388 102.0838
           F24_3    F25_3
Trait 1 103.2643 103.7863

$`Generation 4`
            M1_4     M2_4     M3_4     M4_4     M5_4     M6_4     M7_4     M8_4
Trait 1 101.8188 102.3258 103.1171 102.7379 103.1171 102.7379 104.4223 102.9893
            M9_4    M10_4    M11_4    M12_4    M13_4    M14_4    M15_4    M16_4
Trait 1 103.7681 103.7681 101.5768 103.5167 103.5113 104.1654 104.0431 102.9994
           M17_4    M18_4    M19_4    M20_4    M21_4    M22_4    M23_4    M24_4
Trait 1 102.8625 103.7681 103.3889 102.8852 103.5167 102.3452 102.2207 101.5768
           M25_4     F1_4     F2_4     F3_4     F4_4     F5_4     F6_4     F7_4
Trait 1 102.3258 102.0838 102.2207 103.2417 103.7681 102.8852 101.4522 103.7681
            F8_4     F9_4    F10_4    F11_4    F12_4    F13_4   F14_4    F15_4
Trait 1 101.8415 104.0431 103.3786 102.8522 103.6435 100.9029 102.473 101.8085
           F16_4    F17_4   F18_4    F19_4    F20_4    F21_4    F22_4   F23_4
Trait 1 103.7863 103.7681 102.198 103.7681 104.4404 103.1139 104.0431 102.473
           F24_4    F25_4
Trait 1 102.7379 104.4223

$`Generation 5`
            M1_5     M2_5     M3_5     M4_5     M5_5     M6_5     M7_5     M8_5
Trait 1 103.3889 102.6102 102.7348 103.7681 102.0702 104.0431 102.6102 103.5167
            M9_5    M10_5    M11_5    M12_5    M13_5    M14_5    M15_5    M16_5
Trait 1 102.8625 104.1654 103.7681 102.7244 102.0838 103.5167 103.3889 102.6102
           M17_5    M18_5    M19_5    M20_5    M21_5    M22_5    M23_5    M24_5
Trait 1 102.8625 103.1321 104.1654 103.6435 103.7681 103.7681 103.7681 103.4931
           M25_5     F1_5     F2_5     F3_5     F4_5     F5_5     F6_5    F7_5
Trait 1 104.0431 102.7348 102.8625 103.3889 104.1473 103.5167 102.9893 102.473
            F8_5     F9_5    F10_5    F11_5    F12_5    F13_5    F14_5    F15_5
Trait 1 104.0431 101.6943 104.1473 102.4494 103.2599 104.4223 104.8014 103.5167
           F16_5    F17_5    F18_5    F19_5    F20_5    F21_5    F22_5    F23_5
Trait 1 103.8959 103.3889 103.3889 104.0431 101.5665 103.3889 103.5167 102.2207
           F24_5    F25_5
Trait 1 103.1139 103.7681

MoBPS documentation built on Nov. 9, 2021, 5:08 p.m.