Usage
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")
Arguments
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
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