Visualize metastatic propnesity odds ratio in a volcano plot fashion.

Visualize metastatic propnesity odds ratio in a volcano plot fashion.

Usage

plot_tropism(x, tumor_type)

Arguments

x

An object of class 'INCOMMON' containing the classification results, as produced by function classify.

tumor_type

The tumour type for which classified data is available.

Value

An object or a list of objects of class 'ggplot2'.

Examples

# First load example classified data
data(MSK_classified)
# Estimate the metastatic tropism associated with mutant TP53, PIK3CA and CDH1 with vs without CNA,
# in BRCA, with respect to Liver and Lymph
for(g in c('TP53', 'PIK3CA', 'CDH1')){for(m in c('Liver', 'Lymph')){MSK_classified = met_tropism(x = MSK_classified, gene = g, tumor_type = 'BRCA', metastatic_site = m)}}
#> ℹ There are 20289 different genotypes
#> ℹ The most abundant genotypes are:
#> • Mutant TP53 with LOH (562 Samples, Frequency 0.02)
#> • Mutant KRAS without AMP (199 Samples, Frequency 0.01)
#> • Mutant KRAS without AMP,Mutant TP53 with LOH (149 Samples, Frequency 0.01)
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> # A tibble: 1 × 7
#>   gene  metastatic_site class                   OR   low    up p.value
#>   <chr> <chr>           <chr>                <dbl> <dbl> <dbl>   <dbl>
#> 1 TP53  Liver           Mutant TP53 with LOH  1.36 0.334  9.13   0.699
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> # A tibble: 1 × 7
#>   gene  metastatic_site class                   OR   low    up p.value
#>   <chr> <chr>           <chr>                <dbl> <dbl> <dbl>   <dbl>
#> 1 TP53  Lymph           Mutant TP53 with LOH  2.30 0.422  42.7   0.434
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> # A tibble: 1 × 7
#>   gene   metastatic_site class                     OR   low    up p.value
#>   <chr>  <chr>           <chr>                  <dbl> <dbl> <dbl>   <dbl>
#> 1 PIK3CA Liver           Mutant PIK3CA with AMP  1.30 0.786  2.16   0.310
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> # A tibble: 1 × 7
#>   gene   metastatic_site class                     OR   low    up p.value
#>   <chr>  <chr>           <chr>                  <dbl> <dbl> <dbl>   <dbl>
#> 1 PIK3CA Lymph           Mutant PIK3CA with AMP 0.709 0.390  1.28   0.253
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> # A tibble: 1 × 7
#>   gene  metastatic_site class                   OR   low    up p.value
#>   <chr> <chr>           <chr>                <dbl> <dbl> <dbl>   <dbl>
#> 1 CDH1  Liver           Mutant CDH1 with LOH  1.35 0.465  4.52   0.597
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> # A tibble: 1 × 7
#>   gene  metastatic_site class                   OR    low    up p.value
#>   <chr> <chr>           <chr>                <dbl>  <dbl> <dbl>   <dbl>
#> 1 CDH1  Lymph           Mutant CDH1 with LOH 0.338 0.0998  1.11  0.0716
# Plot results in a volcano plot
plot_tropism(x = MSK_classified, tumor_type = 'BRCA')