phosphomatics module

exception phosphomatics.InvalidKey

Bases: Exception

exception phosphomatics.NoDataSetTokenError

Bases: Exception

exception phosphomatics.NoPhosphomaticsKey

Bases: Exception

class phosphomatics.Phosphomatics(key=None)

Bases: object

Phosphomatics experiment session.

Parameters

key (str) – Phosphomatics API key. Contact the developers to obtain a key.

doKSEAAnslysis(group1=None, group2=None, networkin=None, networkinThreshold=None, mThreshold=None, pThreshold=None, container=None)
getActiveDataGroup()

Get the currently active data group

Returns

Dict containing group information for selected data group.

Dict has keys

  • id (int) - anidentifier for this individual data group

  • name (str) - data group name

  • selected (str) - ‘true’ if the data group is currently active, ‘false’ if not

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

getDataSetToken()

Get the datasetToken for the current analysis.

Returns

DatasetToken for the current analysis

getEnrichmentForProteinList(container=None)
getLDA(pval=0.5, pvalType='raw', fc=0.5, transformation=None)

Returns linear discriminant analysis for data in selected data group.

Parameters

  • pval (float) – p-value used to filter phosphorylation sites prior to analysis. Setting the p-value to 0 will allow all phosphorylation sites to pass. Default = 0.5.

  • pvalType (str) – Either ‘raw’ for raw p-values or ‘BH’ for Benjamini-Hochberg adjusted p-values. Default = ‘raw’.

  • fc (float) – fold-change used to filter phosphorylation sites prior to analysis. Setting this to 0 will allow all phosphorylation sites to pass. In the case of a >2 group analysis, this corresponds to the ANOVA F-value. Default = 0.5.

  • transformation (str) – Specifies if data should be z-transformed prior to analysis. Either ‘Z-Transform’ to conduct transformation or any other value for untransformed data.

Returns

Dict containing LDA data.

Dict has keys

  • data - list of dicts with x,y coordinates of samples on LD1 and LD2 axes. Dicts have keys ‘x’, ‘y’, ‘label’, ‘group’.

  • xLabel - LD axis of x co-ordinates and percentage of explained variation.

  • yLabel - LD axis of y co-ordinates and percentage of explained variation.

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

getPCA(pval=0.5, pvalType='raw', fc=0.5, transformation=None)

Returns Principal Component Analysis for data in selected data group.

Parameters

  • pval (float) – p-value used to filter phosphorylation sites prior to analysis. Setting the p-value to 0 will allow all phosphorylation sites to pass. Default = 0.5.

  • pvalType (str) – Either ‘raw’ for raw p-values or ‘BH’ for Benjamini-Hochberg adjusted p-values. Default = ‘raw’.

  • fc (float) – fold-change used to filter phosphorylation sites prior to analysis. Setting this to 0 will allow all phosphorylation sites to pass. In the case of a >2 group analysis, this corresponds to the ANOVA F-value. Default = 0.5.

  • transformation (str) – Specifies if data should be z-transformed prior to analysis. Either ‘Z-Transform’ to conduct transformation or any other value for untransformed data.

Returns

Dict containing PCA data.

Dict has keys

  • data - list of dicts with x,y coordinates of samples on PC1 and PC2 axes. Dicts have keys ‘x’, ‘y’, ‘label’, ‘group’.

  • xLabel - PC axis of x co-ordinates and percentage of explained variation.

  • yLabel - PC axis of y co-ordinates and percentage of explained variation.

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

getQuantitationPlotForSelectedKinase(specificity=None, kinaseUPID=None, plotType=None, container=None)
getSequenceAnslysis(displayType=None, palette=None, showN=None, container=None)
getUserDataGroups()

Get all data groups that have been created.

Returns

List of dicts containing group information.

Dicts have keys

  • id (int) - anidentifier for this individual data group

  • name (str) - data group name

  • selected (str) - ‘true’ if the data group is currently active, ‘false’ if not

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

makeClusterMap(fc=None, pval=None, pvalType=None, numClusters=None, transformation=None, metric=None, method=None, container=None, targetClusters=None)
makeCorrelationMatrix(method=None, transform=None, container=None)
makeDistributionPlot(sample=None)
makeFeatureAbundancePlot(substrateUPID=None, position=None, residue=None, plotType=None, container=None)
makeKinaseClusterMap(numClusters=None, transformation=None, palette=None, metric=None, method=None, specificity=None, container=None, targetClusters=None)
makeKinaseSCurve(group1=None, group2=None, specificity=None, container=None)
makeKinaseVolcanoPlot(fc=None, pval=None, pvalType=None, group1=None, group2=None, container=None, specificity=None)
makePhosphorylationNetworks(group1=None, group2=None, specificity=None, container=None)
makeQuantilePlot(container=None, sample=None)
makeSCurve(group1=None, group2=None, container=None)
makeSubstrateCorrelationPlot(substrateUPID=None, position=None, residue=None, topN=None, method=None, plotType=None, container=None)
makeVolcano(fc=None, pval=None, pvalType=None, group1=None, group2=None, container=None)
process()

Run initial data processing through phosphomatics. Must be called after uploading Experimental data and processing parameter files.

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

setDataSetToken(datasetToken)

Sets the datasetToken for a prior phosphomatics analysis.

Parameters

datasetToken (str) – An existing phosphomaitcs datasetToken

setSelectedGroup(id=None)

Change the currently active data group.

Parameters

id (int) – Integer id of data group to be selected.

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

startNewExperiment()

Prepare a new experiment on the phosphomatics server and obtain a valid datasetToken.

Returns

DatasetToken for the current analysis

Raises

Exception – Error generating datasetToken.

uploadExperimentalData(file)

Upload phosphorylation site and quantitation data. Data file must be in a phosphomatics-compatible format. See here for details.

Parameters

file (str) – Path to experimental data file.

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

uploadParameterSet(file)

Upload phosphomatics parameter file.

Parameters

file (str) – Path to phosphomatics parameter file.

Raises

NoDataSetTokenError – Raised if method called before a valid datasetToken is obtained or set.

volcano(kwargs)
phosphomatics.get_kwargs()