Description Usage Arguments Details Value

Create a heatmap-like plot showing information about both effect size and p-values.

1 2 3 4 | ```
pvalEffectPlot(e, p, pval.thr = 0.01, pval.cutoff = 1e-06,
row.labels = NULL, col.labels = NULL, plot.func = NULL, grid = "at",
grid.color = "#33333333", plot.cex = 1, text.cex = 1,
col.labels.style = "top", legend.style = "auto")
``` |

`e` |
matrix with effect sizes |

`p` |
matrix with probabilities |

`pval.thr` |
The p-value must be this or lower in order for a test result to be visualized |

`pval.cutoff` |
On visual scale, all p-values below pval.cutoff will be replaced by pval.cutoff |

`row.labels` |
Labels for the modules. This must be a named vector, with module IDs as vector names. If NULL, module titles from the analyses results will be used. |

`col.labels` |
Labels for the columns. If NULL, names of the elements of the list x will be used. |

`plot.func` |
Optionally, a function to be used to draw the dots. See "Details" |

`grid` |
Style of a light-grey grid to be plotted; can be "none", "at" and "between" |

`grid.color` |
Color of the grid to be plotted (default: light grey) |

`plot.cex` |
a numerical value giving the amount by which the plot symbols will be maginfied |

`text.cex` |
a numerical value giving the amount by which the plot text will be magnified, or a vector containing three cex values for row labels, column labels and legend, respectively |

`col.labels.style` |
Style of column names: "top" (default), "bottom", "both", "none" |

`legend.style` |
Style of the legend: "auto" – automatic; "broad": pval legend side by side with effect size legend; "tall": effect size legend above pval legend; "none" – no legend. |

pvalEffectPlot shows a heatmap-like plot. Each row corresponds to one series of tests (e.g. one module), and each column corresponds to the time points or conditions for which a given analysis was run. Each significant result is shown as a red dot. Size of the dot corresponds to the effect size (or any arbitrary value), and intensity of the color corresponds to the log10 of p-value.

Just like a heatmap corresponds to a single numeric matrix, the pvalue / effect plot corresponds to two matrices: one with the effect size, and another one with the p-values. Each cell in the matrix corresponds to the results of a single statistical test.

For example, a number of genes or transcriptional modules might be tested for differential expression or enrichment, respectively, in several conditions.

By default, each test outcome is represented by a dot of varying size and color. Alternatively, a function may be specified with the parameter 'plot.func'. It will be called for each test result to be drawn. The plot.func function must take the following arguments:

row, coleither row / column number or the id of the row / column to plot; NULL if drawing legend

x, yuser coordinates of the result to visualize

w, hwidth and height of the item to plot

eEnrichment – a relative value between 0 and 1, where 0 is the minimum and 1 is the maximum enrichment found

pP-value – an absolute value between 0 and 1

For the purposes of drawing a legend, the function must accept NULL p-value or a NULL enrichment parameter.

Invisibly returns a NULL value.

tmod documentation built on March 18, 2018, 1:59 p.m.

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