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Visualize differential expression results

Source: R/diff_expression.R
hd_plot_volcano.Rd

hd_plot_volcano() creates volcano plots for the differential expression results. It colors and labels the top-n up and down regulated proteins.

Usage

hd_plot_volcano(
  de_object,
  pval_lim = 0.05,
  logfc_lim = 0,
  top_up_prot = 10,
  top_down_prot = 5,
  palette = "diff_exp",
  title = NULL,
  report_nproteins = TRUE,
  user_defined_proteins = NULL
)

Arguments

de_object

The differential expression object. Created by hd_de_limma() or hd_de_ttest().

pval_lim

The p-value limit for significance. Default is 0.05.

logfc_lim

The logFC limit for significance. Default is 0.

top_up_prot

The number of top up regulated proteins to label on the plot. Default is 10.

top_down_prot

The number of top down regulated proteins to label on the plot. Default is 5.

palette

The color palette for the plot. If it is a character, it should be one of the palettes from hd_palettes(). Default is "diff_exp".

title

The title of the plot or NULL for no title.

report_nproteins

If the number of significant proteins should be reported in the title. Default is TRUE.

user_defined_proteins

A vector with the protein names to label on the plot if customization is required. Default is NULL.

Value

A DE object with the volcano plot.

Examples

# Initialize an HDAnalyzeR object
hd_object <- hd_initialize(example_data, example_metadata)

# Run differential expression analysis for AML vs all others
de_results <- hd_de_limma(hd_object, case = "AML")

# Create a volcano plot
hd_plot_volcano(de_results)
#> $de_res
#> # A tibble: 100 × 10
#>    Feature  logFC   CI.L   CI.R AveExpr     t  P.Value adj.P.Val     B Disease
#>    <chr>    <dbl>  <dbl>  <dbl>   <dbl> <dbl>    <dbl>     <dbl> <dbl> <chr>  
#>  1 ADA      1.46   1.17   1.75   0.924   9.83 3.29e-21  3.29e-19 37.3  AML    
#>  2 AZU1     1.53   1.20   1.86   0.226   9.10 1.32e-18  6.62e-17 31.4  AML    
#>  3 APEX1    1.56   1.17   1.95   0.517   7.90 1.40e-14  4.67e-13 22.3  AML    
#>  4 APBB1IP  1.17   0.855  1.49  -0.237   7.24 1.48e-12  3.69e-11 17.8  AML    
#>  5 ANGPT1  -1.70  -2.18  -1.21   1.72   -6.92 1.24e-11  2.48e-10 15.6  AML    
#>  6 ADGRG1   1.23   0.837  1.63   1.54    6.12 1.75e- 9  2.92e- 8 10.8  AML    
#>  7 ANGPT2   0.773  0.522  1.02   0.920   6.04 2.70e- 9  3.86e- 8 10.3  AML    
#>  8 ARTN     0.829  0.552  1.11   0.429   5.88 6.95e- 9  8.69e- 8  9.47 AML    
#>  9 APP     -0.823 -1.15  -0.493  1.17   -4.90 1.24e- 6  1.35e- 5  4.42 AML    
#> 10 AGRP     0.756  0.452  1.06   0.0229  4.88 1.35e- 6  1.35e- 5  4.35 AML    
#> # ℹ 90 more rows
#> 
#> $volcano_plot

#> 
#> attr(,"class")
#> [1] "hd_de"