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.
saveProgenyPlots(plots, contrast_names, dirpath)
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. |
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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 |
This function produces the pdf files of plots taken from the progenyScatter function
#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)#> Warning: Removed 10 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 10 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 10 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 8 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 9 rows containing missing values (geom_label_repel).#> Warning: 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missing values (geom_hline).#> Warning: Removed 6 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 9 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 10 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 11 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 10 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 8 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> Warning: Removed 9 rows containing missing values (geom_label_repel).#> Warning: Removed 1 rows containing missing values (geom_hline).#> 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