Description Usage Arguments Details Author(s) Examples

View source: R/EDA_functions.R

Given a SpC matrix and a two levels factor, draws a scatterplot with SpC means of one condition in the x axis and SpC means of the second condition in the y axis.

1 | ```
spc.scatterplot(msms.counts, treat, trans="log2", minSpC=2, minLFC=1, ...)
``` |

`msms.counts` |
A SpC matrix with proteins in the rows and samples in the columns. |

`treat` |
A two level factor of length equal to the number of columns in the expression matrix. The two levels represent the conditions to be compared. |

`trans` |
The transformation made on the means before plotting. One among "log2", "sqrt", or "none". The default is "log2". |

`minSpC` |
Used as signal threshold. |

`minLFC` |
Used as size effect threshold. |

`...` |
Extra parameters passed to the plot function. |

The transformed means are plotted, one condition versus the other. The borders
representing absolute log fold change 1 are drawn as dashed lines.
All features with log fold change equal to or greather than `minLFC`

and with
mean SpC in the most abundant condition equal to or greather than `minSpC`

are colored in red.

Josep Gregori

1 2 3 | ```
data(msms.dataset)
spc.scatterplot(exprs(msms.dataset),treat=pData(msms.dataset)[,1],trans="log2",
minSpC=2,minLFC=1,main="UPS1 200fm vs 600fm")
``` |

msmsEDA documentation built on Nov. 1, 2018, 3:59 a.m.

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