3 Grouping `ppp`-Hypercolumn

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Note

The examples in Chapter 3 require

library(groupedHyperframe)
library(survival)

Listing 3.1 creates a grouped hyper data frame s with one-and-only-one point-pattern (ppp, Chapter 24) hypercolumn from the data frame wrobel_lung. This process (Chapter 31)

takes a data frame wrobel_lung as input;
creates a point-pattern hypercolumn ppp. from the \(x\)- and \(y\)-coordinates, the numeric mark hladr and the multi-type mark phenotype, per image_id nested within patient_id;
aggregates other variables of interest, e.g., OS, gender and age, at the level of image_id nested within patient_id. Those variables must be identical within the nested grouping structure ~patient_id/image_id;
returns a grouped hyper data frame s.

Listing 3.1: Create a grouped hyper data frame with one-and-only-one ppp-hypercolumn

s = wrobel_lung |>
   grouped_ppp(
     formula = hladr + phenotype ~ OS + gender + age, 
     by = ~ patient_id/image_id
   )

Readers may view the grouped hyper data frame s (Listing 3.1) by simply typing s at the R console prompt and pressing Enter (Listing 3.2),

Listing 3.2: View grouped hyper data frame s (Listing 3.1)

Grouped Hyper Data Frame: ~patient_id

3 patient_id

      OS gender age    patient_id          image_id  ppp.
1    176      M  84 #03 2-080-378 [36953,13765].im3 (ppp)
2    176      M  84 #03 2-080-378 [39206,15250].im3 (ppp)
3    176      M  84 #03 2-080-378 [40242,17359].im3 (ppp)
4    176      M  84 #03 2-080-378 [40863,16444].im3 (ppp)
5  3488+      F  85 #01 0-889-121 [40864,18015].im3 (ppp)
6    176      M  84 #03 2-080-378 [41191,13764].im3 (ppp)
7  3488+      F  85 #01 0-889-121 [42689,19214].im3 (ppp)
8  3488+      F  85 #01 0-889-121 [42806,16718].im3 (ppp)
9  3488+      F  85 #01 0-889-121 [44311,17766].im3 (ppp)
10 3488+      F  85 #01 0-889-121 [45366,16647].im3 (ppp)
11  1605      M  66 #02 1-037-393 [56576,16907].im3 (ppp)
12  1605      M  66 #02 1-037-393 [56583,15235].im3 (ppp)
13  1605      M  66 #02 1-037-393 [57130,16082].im3 (ppp)
14  1605      M  66 #02 1-037-393 [57396,17896].im3 (ppp)
15  1605      M  66 #02 1-037-393 [57403,16934].im3 (ppp)

Also, readers may view the summary information of the grouped hyper data frame s (Listing 3.1) using the function summary() (Listing 3.3),

Listing 3.3: Summarized information of grouped hyper data frame s (Listing 3.1)

s |> 
  summary()

Grouped Hyper Data Frame: ~patient_id

3 patient_id

                OS         gender        age                patient_id
            (Surv)         (factor) (numeric)                 (factor)
 <time-to-event> :(Surv)   F: 5     Min.   :66.00   #01 0-889-121:5   
 [right-censored]:5        M:10     1st Qu.:66.00   #02 1-037-393:5   
 [observed]      :10                Median :84.00   #03 2-080-378:5   
                                    Mean   :78.33                     
                                    3rd Qu.:85.00                     
                                    Max.   :85.00                     
                                                                      
              image_id ppp. 
              (factor) (ppp)
 [36953,13765].im3:1        
 [39206,15250].im3:1        
 [40242,17359].im3:1        
 [40863,16444].im3:1        
 [40864,18015].im3:1        
 [41191,13764].im3:1        
 (Other)          :9

Readers must note that Chapter 2 and Chapter 3 describe two independent approaches to

create a grouped hyper data frame, from a data frame (Chapter 2, Listing 2.2, Section 12.1);
create a grouped hyper data frame with one-and-only-one point-pattern hypercolumn, from a data frame (Chapter 3, Listing 3.1, Chapter 31).

These two approaches are independent and unrelated to each other (Section 40.1).