View source: R/qc_ranked_intensities.R
qc_ranked_intensities | R Documentation |
Calculates and plots ranked intensities for proteins, peptides or precursors.
qc_ranked_intensities( data, sample, grouping, intensity_log2, facet = FALSE, plot = FALSE, y_axis_transformation = "log10", interactive = FALSE )
data |
a data frame that contains at least sample names, grouping identifiers (precursor, peptide or protein) and log2 transformed intensities for each grouping identifier. |
sample |
a character column in the |
grouping |
a character column in the |
intensity_log2 |
a numeric column in the |
facet |
a logical value that specifies whether the calculation should be done group wise by
sample and if the resulting plot should be faceted by sample. (default is |
plot |
a logical value that specifies whether the result should be plotted (default is |
y_axis_transformation |
a character value that determines that y-axis transformation. The value is either "log2" or "log10" (default is "log10"). |
interactive |
a logical value that specifies whether the plot should be interactive
(default is |
A data frame containing the ranked intensities is returned. If plot = TRUE
a plot
is returned. The intensities are log10 transformed for the plot.
set.seed(123) # Makes example reproducible # Create synthetic data data <- create_synthetic_data( n_proteins = 50, frac_change = 0.05, n_replicates = 4, n_conditions = 3, method = "effect_random", additional_metadata = FALSE ) # Plot ranked intensities for all samples combined qc_ranked_intensities( data = data, sample = sample, grouping = peptide, intensity_log2 = peptide_intensity, plot = TRUE, ) # Plot ranked intensities for each sample separately qc_ranked_intensities( data = data, sample = sample, grouping = peptide, intensity_log2 = peptide_intensity, plot = TRUE, facet = TRUE )
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