View source: R/protPepProfilePlot.R

This function plots the average profiles of any protein in the dataset, the peptide profiles, and also the reference profile for each compartment

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
protPepPlotfun(
protName,
protProfileSummary,
Nspectra = T,
finalList = NULL,
protPepData = NULL,
refCol = 5,
n.fractions = 9,
n.compartments = 8,
markerLocR = markerLocRuse,
assignPropsMat = assignPropsUse,
propCI = F,
transType = "",
yAxisLabel = ""
)
``` |

`protName` |
Name of the protein to plot |

`protProfileSummary` |
data frame of protein names and their relative abundance levels.. |

`Nspectra` |
indicator for if there are columns in protProfileSummary for Nspectra (number of spectra) and Npep (number of peptides) |

`finalList` |
spectrum-level abundance levels by protein and peptide; Ehis is NULL if not available |

`n.fractions` |
number of fractions per protein |

`n.compartments` |
number of compartments (8 in Jadot data) |

`markerLocR` |
A matrix markerLocR giving the abundance level profiles of the subcellular locations n.compartments = 8 columns are subcellular locations, and n.fractions rows are the fraction names |

`assignPropsMat` |
A matrix of assignment proportions, from the constrained proportional assignment algorithm, and optionally upper and lower 95 percent confidence limits |

`propCI` |
True if lower and upper confidence intervals are included in assignPros |

`refLocProteins` |
List of reference proteins |

`predictedProp.mat` |
A matrix of CPA predicted proportions, from proLocAll |

`confint` |
indicator for if there are standard errors (from bootstrapping) for the assigned proportions (in protProfileSummary) |

`predictedPropL.mat` |
Matrix of lower confidence limits, one row for each protein, and 9 columns of lower confidence interval limits |

`predictedPropU.mat` |
Matrix of upper confidence limits, one row for each protein, and 9 columns of upper confidence interval limits |

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