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Plot differential regressions for a link

Source: R/plotting_functions.R
plot_regressions.Rd

Plot differential regressions for any target-target pair in an omic dataset

Usage

plot_regressions(
  deggs_object,
  assayDataName = 1,
  gene_A,
  gene_B,
  title = NULL,
  legend_position = "topright"
)

Arguments

deggs_object

an object of class deggs generated by get_diffNetworks

assayDataName

name of the assayData of interest. If an unnamed list of data was given to get_diffNetworks, the assayDataName here will be the number indicating the position of the data in the assayDataList provided before (i.e. if the user wants to plot a differential interaction observed in the transcriptomic data, which was second in the list, then assayDataName must be 2, if only one data table was provided assayDataName must be 1). Default 1.

gene_A

character. Name of the first target (gene, protein, metabolite, etc.)

gene_B

character. Name of the second target (gene, protein, metabolite, etc.)

title

plot title. If NULL (default), the name of the assayData will be used. Use empty character "" for no title.

legend_position

position of the legend in the plot. It can be specified by keyword or in any parameter accepted by xy.coords (defalut "topright")

Value

base graphics plot showing differential regressions across categories. The p value of the interaction term of gene A ~ gene B \* category is reported on top.

Examples

data("synthetic_metadata")
data("synthetic_rnaseqData")
data("synthetic_proteomicData")
data("synthetic_OlinkData")
assayData_list <- list("RNAseq" = synthetic_rnaseqData,
                       "Proteomics" = synthetic_proteomicData,
                       "Olink" = synthetic_OlinkData)
deggs_object <- get_diffNetworks(assayData = assayData_list,
                                 metadata = synthetic_metadata,
                                 category_variable = "response",
                                 regression_method = "lm",
                                 padj_method = "bonferroni",
                                 verbose = FALSE,
                                 show_progressBar = FALSE,
                                 cores = 1)
plot_regressions(deggs_object,
                 assayDataName = "RNAseq",
                 gene_A = "MTOR", 
                 gene_B = "AKT2",
                 legend_position = "bottomright")