Plot the index of Divergent Evolutionary Trajectories.

Plot the index of Divergent Evolutionary Trajectories, for a set of drivers using function DET_index. The plot is a barplot with colours reflecting the number of distinct incoming edges in each driver (species), and the height reflecting the actual DET index value.

plot_DET_index(x, ...)

Arguments

x

A REVOLVER object with fits.

...

Parmeters passed to function DET_index in order to compute the index value.

Value

A `ggplot` object of the plot.

See also

Other Plotting functions: distinct_palette_few(), distinct_palette_many(), gradient_palette(), plot_clusters(), plot_dendrogram(), plot_drivers_clonality(), plot_drivers_graph(), plot_drivers_occurrence(), plot_jackknife_cluster_stability(), plot_jackknife_coclustering(), plot_jackknife_trajectories_stability(), plot_patient_CCF_histogram(), plot_patient_data(), plot_patient_mutation_burden(), plot_patient_oncoprint(), plot_patient_trees_scores()

Examples

# Data released in the 'evoverse.datasets'
data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets')

plot_DET_index(TRACERx_NEJM_2017_REVOLVER)
#> # A tibble: 79 × 4
#>    driver diversity     N DET_index
#>    <chr>      <dbl> <int>     <dbl>
#>  1 APC            0     1         0
#>  2 BRAF           0     1         0
#>  3 CDKN2A         0     1         0
#>  4 CHEK2          0     1         0
#>  5 CIC            0     1         0
#>  6 CMTR2          0     1         0
#>  7 COL2A1         0     1         0
#>  8 CREBBP         0     1         0
#>  9 CUX1           0     1         0
#> 10 DICER1         0     1         0
#> # ℹ 69 more rows


# Passing parameters to DET_index
plot_DET_index(TRACERx_NEJM_2017_REVOLVER, min.occurrences = 5)
#> # A tibble: 17 × 4
#>    driver diversity     N DET_index
#>    <chr>      <dbl> <int>     <dbl>
#>  1 CDKN2A     0         1     0    
#>  2 COL2A1     0         1     0    
#>  3 EGFR       0         1     0    
#>  4 FAT1       0         1     0    
#>  5 FGFR1      0         1     0    
#>  6 KEAP1      0         1     0    
#>  7 MYC        0         1     0    
#>  8 NFE2L2     0         1     0    
#>  9 NOTCH1     0         1     0    
#> 10 PIK3CA     0         1     0    
#> 11 PTEN       0         1     0    
#> 12 RASA1      0         1     0    
#> 13 SOX2       0         1     0    
#> 14 STK11      0         1     0    
#> 15 TERT       0         1     0    
#> 16 KRAS       0.598     2     0.863
#> 17 TP53       1.42      5     0.880