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protti

volcano_protti

Volcano plot

Description

Plots a volcano plot for the given input.

Usage

volcano_protti(
  data,
  grouping,
  log2FC,
  significance,
  method,
  target_column = NULL,
  target = NULL,
  facet_by = NULL,
  title = "Volcano plot",
  x_axis_label = "log2(fold change)",
  y_axis_label = "-log10(q-value)",
  legend_label = "Target",
  log2FC_cutoff = 1,
  significance_cutoff = 0.01,
  interactive = FALSE
)

Arguments

`data`	a data frame containing at least the input variables.
`grouping`	the column in the data data frame containing either precursor or peptide identifiers.
`log2FC`	the column in the data frame containing the log2 transfromed fold changes between two conditions.
`significance`	the column containing the p-value or adjusted p-value for the corresponding fold changes. P-value is ideally adjusted using e.g. Benjamini-Hochberg correction.
`method`	character verctor with the method used for the plot. `method = "target"` highlights your protein, proteins or any other entities of interest (specified in the 'target' argument) in the volcano plot. `method = "significant"` highlights all significantly changing entities.
`target_column`	optional column required for `method = "target"`, can contain for example protein identifiers or a logical that marks certain proteins such as proteins that are known to interact with the treatment. Can also be provided if `method = "significant"` to label data points in an interactive plot.
`target`	optional character vector argument required for `method = "target"`. It can contain one or more specific entities of the column provided in `target_column`. This can be for example a protein ID if `target_column` contains protein IDs or TRUE or FALSE for a logical column.
`facet_by`	optional argument specifying a column that contains information by which the data should be faceted into multiple plots.
`title`	optional argument specifying the title of the volcano plot. Default is "Volcano plot".
`x_axis_label`	optional argument specifying the x-axis label. Default is "log2(fold change)".
`y_axis_label`	optional argument specifying the y-axis label. Default is "-log10(q-value)".
`legend_label`	optional argument specifying the legend label. Default is "Target".
`log2FC_cutoff`	optional argument specifying the log2 transformed fold change cutoff used for assessing whether changes are significant. Default value is 1.
`significance_cutoff`	optional argument specifying the p-value cutoff used for assessing significance of changes. Default is 0.01.
`interactive`	logical, indicating whether the plot should be interactive or not. Default is `interactive = FALSE`.

Value

Depending on the method used a volcano plot with either highlighted targets (method = "target") or highlighted significant proteins (method = "significant") is returned.

Examples

## Not run: 
volcano_protti(
  data,
  grouping = pep_stripped_sequence,
  log2FC = log2FC,
  significance = p_value,
  method = "target",
  target_column = uniprot_id,
  target = "Q9Y6K9",
  facet_by = comparison,
  title = "Finding Nemo",
  x_axis_label = "log2(fold change) treated vs untreated",
  y_axis_label = "-log10(p-value)",
  legend_label = "Target Protein",
  log2FC_cutoff = 2,
  significance_cutoff = 0.05,
  interactive = TRUE
)

## End(Not run)

protti

Bottom-Up Proteomics and LiP-MS Quality Control and Data Analysis Tools

v0.1.1

MIT + file LICENSE

Authors

Jan-Philipp Quast [aut, cre], Dina Schuster [aut], ETH Zurich [cph, fnd]

Initial release

volcano_protti

Description

Usage

Arguments

Value

Examples

protti

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