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.
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
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)
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#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)