create_overview_plot: Overview plot
In gCMAPWeb: A web interface for gene-set enrichment analyses

Description Usage Arguments Value Author(s)

This function creates an overview density plot summarizing the similarity scores obtained for all instances in the reference database.

create_overview_plot(effect.sample, effect.population, file.name,
  reference.name, main = "Distribution of similarity scores",
  xlab = "Effect size", col.set = "black", col.up = "#1B9E77",
  col.down = "blue", strip.cutoffs = c(-3, 3), strip.bounds = c(-6, 6),
  strip.col = c("#1B9E77", "white", "blue"), url.base = NULL,
  up.label = "Correlated", down.label = "Anti-correlated")

`effect.sample`	numeric, the scores for all gene sets in the reference database deemed significantly similar
`effect.population`	numeric, the scores for all gene sites in the reference database
`file.name`	character, path and name of the output file
`reference.name`	name of the reference dabatase
`main`	main title of the plot
`xlab`	x-axis label
`col.set`	color used for the significant samples in the density plot
`col.up`	color used to indicate significantly correlated / enriched gene sets in the rug plot
`col.down`	color used to indicate significantly anti-correlated / depleted gene sets in the rug plot
`strip.cutoffs`	numeric vector, indicating the area of the heat-strip set to the intermediat strip.col. Default=c(-3,3)
`strip.bounds`	numeric vector, indicating the cutoffs above / below which the color of the heat-strip is set to maximum. Default=c(-6,6)
`strip.col`	character vector with three elements, indicating high, neutral and low scores, respectively. Default=c("#1B9E77", "white", "blue")
`url.base`	path the location of the output files relative to the gCMAPWeb home directory
`up.label`	character, legend label for positive scores
`down.label`	character, legend label for negative scores