R package:blupADC-Feature 5

Overview

🦄 An intuitive and clear structure of pedigree could help breeders to make better decision in breeding plan. By applying ggped function, user can plot the structure of pedigree in an easy way.

Example

Plot whole pedigree

library(blupADC)
pedigree_result=ggped(
                input_pedigree=example_ped2
                ) 

Plot subset of whole pedigree

library(blupADC)
pedigree_result=ggped(
                input_pedigree=example_ped2,
    			trace_id=c("121")             #provided subset-id
                )                   

Plot subset of whole pedigree (with sibs)

library(blupADC)
pedigree_result=ggped(
                input_pedigree=example_ped2,
    			trace_id=c("121"),
    			trace_sibs=TRUE   #whether plot the sibs of subset-id  
                )                   

Change the style of picture

User can change the style of pedigree by modifying the shape_type parameter. Default shape_type is 4.

Output

The output of ggped is the object of ggplot, user can plot the pedigree structure or save it directly.

Parameter

💥Basic

• 1：input_pedigree

User-provided pedigree data, data.frame or matrix class.

💌The format of provided pedigree data should be 3 columns format:

• 2: trace_id

Individuals set in tracing pedigree, character class. Default is NULL (plot whole individuals in pedigree)

• 3: trace_sibs

Whether tracing the sibs of individuals set , logical class. Default is FALSE .

• 4: ind_sex

Sex record of individuals , data.frame class.

The format of this data is showing as follow:

For individual who doesn’t have the record of sex, the sex of this individual would be set as Male.

• 5：plot_family

Whether showing family structure when plotting the pedigree, logical class. Default is FALSE .

• 6：shape_type

The shape type when plotting pedigree ，numeric class. Default is 4.

💨Advanced

• 7: shape_size

The shape size of picture, numeric class. Default is 8 .

• 8：ind_text_size

The size of individual name, numeric class. Default is 4 .

• 9：ind_text_vjust

The vjust of individual name, numeric class. Default is 3 .