Analysis tables and plots of expression values
analyze_enrichments.Rd
analyze_enrichments()
is a GGplot2 implementation for plotting the expression differences
as foldchange ~ statistical significance. See also plot_proportion()
. This function can
take either a tidyproteomics data object or a table with the required headers.
Usage
analyze_enrichments(
data = NULL,
top_n = 50,
significance_max = 0.05,
enriched_up_color = "blue",
enriched_down_color = "red",
height = 6.5,
width = 10
)
Arguments
- data
a character defining the column name of the log2 foldchange values.
- top_n
a numerical value defining the number of terms to display in the plot
- significance_max
a numeric defining the maximum statistical significance to highlight.
- enriched_up_color
a color to assign the up enriched values
- enriched_down_color
a color to assign the down enriched values
- width
a numeric
Examples
library(dplyr, warn.conflicts = FALSE)
library(tidyproteomics)
hela_proteins %>%
expression(knockdown/control) %>%
analyze_expressions(log2fc_min = 0.5, significance_column = "p_value")
#> ℹ .. expression::t_test testing knockdown / control
#> ✔ .. expression::t_test testing knockdown / control [3.3s]
#>
#> ℹ Saved plot_volcano.png
#>
#> ── Quantitative Proteomics Data Object ──
#>
#> Origin ProteomeDiscoverer
#> proteins (11.40 MB)
#> Composition 6 files
#> 2 samples (control, knockdown)
#> Quantitation 7055 proteins
#> 4 log10 dynamic range
#> 28.8% missing values
#> *imputed
#> Accounting (4) num_peptides num_psms num_unique_peptides imputed
#> Annotations (9) description biological_process cellular_component molecular_function
#> gene_id_entrez gene_name wiki_pathway reactome_pathway
#> gene_id_ensemble
#> Analyses (1)
#> knockdown/control -> expression
#>