motif.enrichment.plot {ELMER} | R Documentation

## motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs

### Description

motif.enrichment.plot to plot bar plots showing motif enrichment ORs and 95% confidence interval for ORs. Option motif.enrichment can be a data frame generated by `get.enriched.motif` or a path of XX.csv saved by the same function.

### Usage

    motif.enrichment.plot(motif.enrichment,
                          significant = NULL,
                          dir.out ="./",
                          save = TRUE,
                          label = NULL,
                          title = NULL,
                          width = 10,
                          height = NULL,
                          summary = FALSE)

### Arguments

`motif.enrichment` | A data frame or a file path of get.enriched.motif output motif.enrichment.csv file.
`significant` | A list to select subset of motif. Default is NULL.
`dir.out` | A path specify the directory to which the figures will be saved. Current directory is default.
`save` | A logic. If true (default), figure will be saved to dir.out.
`label` | A character. Labels the outputs figure.
`title` | Plot title. Default: no title
`width` | Plot width
`height` | Plot height. If NULL a default value will be calculated
`summary` | Create a summary table along with the plot, it is necessary to add two new columns to object (NumOfProbes and PercentageOfProbes)

### Details

motif.enrichment If input data.frame object, it should contain "motif", "OR", "lowerOR", "upperOR" columns. motif specifies name of motif; OR specifies Odds Ratio, lowerOR specifies lower boundary of OR (95 upperOR specifies upper boundary of OR(95

significant A list used to select subset of motif.enrichment by the cutoff of OR, lowerOR, upperOR. significant=list(OR=1). More than one cutoff can be specified such as significant = list(OR=1, lowerOR=1,upperOR=4)

### Value

A figure shows the enrichment level for selected motifs.

### Author(s)

Lijing Yao (creator: lijingya@usc.edu)

### References

Yao, Lijing, et al. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes." Genome biology 16.1 (2015): 1.

### Examples

    motif.enrichment <- data.frame(motif = c("TP53","NR3C1","E2F1","EBF1","RFX5","ZNF143", "CTCF"),
                                   OR = c(19.33,4.83,1, 4.18, 3.67,3.03,2.49),
                                   lowerOR = c(10,3,1.09,1.9,1.5,1.9, 0.82),
                                   upperOR = c(23,5,3,7,6,5,5),
                                   stringsAsFactors = FALSE)
    motif.enrichment.plot(motif.enrichment = motif.enrichment,
                          significant = list(OR = 3),
                          label = "hypo", save = FALSE)
    motif.enrichment.plot(motif.enrichment = motif.enrichment,
                          significant = list(OR = 3),
                          label = "hypo",
                          title = "OR for paired probes hypomethylated in Mutant vs WT",
                          save = FALSE)
    motif.enrichment <- data.frame(motif = c("TP53","NR3C1","E2F1","EBF1","RFX5","ZNF143", "CTCF"),
                                   OR = c(19.33,4.83,1, 4.18, 3.67,3.03,2.49),
                                   lowerOR = c(10,3,1.09,1.9,1.5,1.5, 0.82),
                                   upperOR = c(23,5,3,7,6,5,5),
                                   NumOfProbes = c(23,5,3,7,6,5,5),
                                   PercentageOfProbes = c(0.23,0.05,0.03,0.07,0.06,0.05,0.05),
                                   stringsAsFactors=FALSE)
    motif.enrichment.plot(motif.enrichment = motif.enrichment,
                          significant = list(OR = 3),
                          label = "hypo", save = FALSE)
    motif.enrichment.plot(motif.enrichment = motif.enrichment,
                          significant = list(OR = 3),
                          label = "hypo",
                          summary = TRUE,
                          title = "OR for paired probes hypomethylated in Mutant vs WT",
                          save = TRUE)

[Package ELMER version 2.11.1 Index]