saveProgenyPlots: Function to save Progeny plots

In saezlab/progeny: Pathway RespOnsive GENes for activity inference from gene expression

Function to save Progeny plots

Description

This function is designed to save the plots (in pdf format) of a nested (2 level) list of arrangeGrob objects, such as the one returned by the progenyScatter function.

Usage

saveProgenyPlots(plots, contrast_names, dirpath)

Arguments

plots	a list of list of arrangeGrob object (such as the one returned by the progenyScatter function.).The first level list elements correspond to samples/contrasts. The second level corresponds to pathways. The plots can be saved in a pdf format using the saveProgenyPlots function.
contrast_names	a vector of the same length as the first level of the plot list corresponding to the names of each sample/contrast
dirpath	the path to the directory where the plots should be saved

Value

This function produces the pdf files of plots taken from the progenyScatter function

Examples

#create plots using progneyScatter function
gene_expression <- read.csv(system.file("extdata", 
"human_input.csv", package = "progeny"))

# getting a weight_matrix
weight_matrix <- getModel("Human", top=100)
weight_matrix <- data.frame(names = row.names(weight_matrix), 
  row.names = NULL, weight_matrix) 
plots <- progenyScatter(gene_expression, weight_matrix)

#create a list with contrast names
contrast_names <- names(gene_expression[2:ncol(gene_expression)])

#assign a path to store your plots
dirpath <- "./progeny_plots/"

# save it
# saveProgenyPlots(plots, contrast_names, dirpath)

saezlab/progeny documentation built on Feb. 9, 2023, 2:21 p.m.