# 4.4 - Regulatory TF plots

# TF ranking plot

For a given enriched motif, all human TF are ranked by the statistical −log10(P−value) assessing the anti-correlation level of candidate Master Regulator TF expression with average DNA methylation level for sites with the given motif. As a result, the most anti-correlated TFs will be ranked in the first positions. By default, the top 3 most anti-correlated TFs and all TF classified by TFClass database in the same (sub)family are highlighted with colors blue, red and orange, respectively.

## TF ranking plot: family classification

Shown are TF ranking plots based on the score (−log10(Pvalue)) of association between TF expression and DNA methylation of an enriched motif in the LUSC cancer type. The dashed line indicates the boundary of the top 5% association score. The top 3 associated TFs and the TF family members=(dots in red) that are associated with that specific motif are labeled in the plot

    load("result/getTF.hypo.TFs.with.motif.pvalue.rda")
    motif <- colnames(TF.meth.cor)[1]
    TF.rank.plot(
      motif.pvalue = TF.meth.cor,
      motif = motif,
      save = FALSE
    )

    ## Retrieving TFClass family classification from ELMER.data.

    ## Retrieving TFClass subfamily classification from ELMER.data.

    ## |                                                    |  0%                      |====================================================|100% ~0 s remaining       |====================================================|100%                      Completed after 0 s

    ## $HXA9_HUMAN.H11MO.0.B

    ## Warning: ggrepel: 66 unlabeled data points (too many overlaps). Consider
    ## increasing max.overlaps

TF ranking plot: For a given enriched motif, all human TF are ranked by the statistical −log10(P−value) assessing the anti-correlation level of candidate Master Regulator TF expression with average DNA methylation level for sites with the given motif. As a result, the most anti-correlated TFs will be ranked in the first positions. By default, the top 3 most anti-correlated TFs, and all TF classified by TFClass database in the same family and subfamily are highlighted with colors blue, red and orange, respectively.

    ##
    ## attr(,"split_type")
    ## [1] "array"
    ## attr(,"split_labels")
    ##   X1
    ## 1  1