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Rank Reponse Plot

Chase Mateusiak

08/04/2022

Rank_Response_Plot.Rmd

Abstract

Create a Rank Response Plot brentlabRnaSeqTools package version: 0.0.0.0

Creating a Rank-Response plot

You will need the following:

  • The expression data you wish to use – there may be more than one (eg, kemmeren data, data from our lab, etc, …)

  • The binding data you wish to use – again, there may be more than one. For instance, maybe you are comparing chip-chip to calling cards

Check ?rank_response_plot for more information on what columns must exist in the expression and binding data.

An example of creating the plots is below:

expr_list = list(
  expr1 = read_csv("~/Desktop/zev_deseq_res.csv"),
  expr2 = read_csv("~/Desktop/zev_deseq_res2.csv")
)

binding_list = list(
  binding1 = read_tsv("~/Desktop/tmp/E0001_HAP2_JP008.sig_prom.txt") %>%
    dplyr::rename(gene = `Systematic Name`,
                  binding_signal = `Poisson pvalue`) %>%
    dplyr::select(gene, binding_signal),
  binding2 = read_tsv("~/Desktop/tmp/E0001_PHO4_JP008.sig_prom.txt") %>%
    dplyr::rename(gene = `Systematic Name`,
                  binding_signal = `Poisson pvalue`) %>%
    dplyr::select(gene, binding_signal)
)

rank_response_plot(expr_list, binding_list, 'test', lfc_thres = 0, padj_thres = .8)

Caveat: I haven’t implemented the random response line yet. However, that can be added – what is returned is a ggplot object. Add it with geom_abline