plot_regressions {multiDEGGs} | R Documentation |
Plot differential regressions for a link
Description
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 |
assayDataName |
name of the assayData of interest. If an unnamed list of
data was given to |
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 |
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")