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_PAAD_output)
# Estimate the metastatic tropism associated with mutant TP53, KRAS, CDKN2A, high vs balanced mutant dosage.
for(g in c('TP53', 'KRAS', 'CDKN2A')){for(m in c('Liver', 'Lymph', 'Bone', 'CNS/Brain')){MSK_PAAD_output = met_tropism(x = MSK_PAAD_output, gene = g, tumor_type = 'PAAD', metastatic_site = m)}}
#> Joining with `by = join_by(id)`
#> 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           High Dosage 0.650 0.410  1.03  0.0664
#> 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           High Dosage  1.24 0.362  3.96   0.716
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: collapsing to unique 'x' values
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: collapsing to unique 'x' values
#> # A tibble: 1 × 7
#>   gene  metastatic_site class          OR   low    up p.value
#>   <chr> <chr>           <chr>       <dbl> <dbl> <dbl>   <dbl>
#> 1 TP53  Bone            High Dosage  1.00    NA    NA   1.000
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: algorithm did not converge
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: collapsing to unique 'x' values
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: algorithm did not converge
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: collapsing to unique 'x' values
#> # A tibble: 1 × 7
#>   gene  metastatic_site class               OR   low    up p.value
#>   <chr> <chr>           <chr>            <dbl> <dbl> <dbl>   <dbl>
#> 1 TP53  CNS/Brain       High Dosage 115193308.     0    NA   0.997
#> 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 KRAS  Liver           High Dosage  1.72  1.09  2.77  0.0232
#> 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 KRAS  Lymph           High Dosage 0.825 0.287  2.10   0.699
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: collapsing to unique 'x' values
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: collapsing to unique 'x' values
#> # A tibble: 1 × 7
#>   gene  metastatic_site class               OR   low    up p.value
#>   <chr> <chr>           <chr>            <dbl> <dbl> <dbl>   <dbl>
#> 1 KRAS  Bone            High Dosage 114425353.     0    NA   0.997
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> # A tibble: 1 × 7
#>   gene  metastatic_site class                 OR   low    up p.value
#>   <chr> <chr>           <chr>              <dbl> <dbl> <dbl>   <dbl>
#> 1 KRAS  CNS/Brain       High Dosage 0.0000000170    NA   Inf   0.998
#> 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 CDKN2A Liver           High Dosage  1.08 0.396  2.68   0.872
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> # A tibble: 1 × 7
#>   gene   metastatic_site class          OR   low    up p.value
#>   <chr>  <chr>           <chr>       <dbl> <dbl> <dbl>   <dbl>
#> 1 CDKN2A Lymph           High Dosage 0.770 0.108  15.4   0.819
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
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#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> # A tibble: 1 × 7
#>   gene   metastatic_site class                  OR   low    up p.value
#>   <chr>  <chr>           <chr>               <dbl> <dbl> <dbl>   <dbl>
#> 1 CDKN2A Bone            High Dosage 0.00000000412    NA   Inf   0.996
# Plot results in a volcano plot
plot_tropism(x = MSK_PAAD_output, tumor_type = 'PAAD')