This function takes two data frames which are outputs from the simpleScore() function and plots the relationship between the two gene set scores for samples in the gene expression matrix.Scoredf1 and Scoredf2 are two scoring results of the same set of samples against two different gene signatures. If you wish to use the plotting function but with some customized inputs (instead of outputs from the simpleScore function), you need to make sure the formats are the same To be specific, you need to have column names "TotalScore" "TotalDispersion" "UpScore" "UpDispersion" "DownScore" "DownDispersion" and rows names as samples.

plotScoreLandscape(
  scoredf1,
  scoredf2,
  scorenames = c(),
  textSize = 1.2,
  isInteractive = FALSE,
  hexMin = 100
)

Arguments

scoredf1

data.frame, result of the simpleScore() function which scores the gene expression matrix against a gene set of interest

scoredf2

data.frame, result of the simpleScore() function which scores the gene expression matrix against another gene set of interest

scorenames

character vector of length 2, names for the two scored gene set/signatures stored in scoredf1 and scoredf2

textSize

numeric, set the text size for the plot, default as 1.5

isInteractive

boolean, whether the plot is interactive default as FALSE

hexMin

integer, the threshold which decides whether hex bin plot or scatter plot is displayed, default as 100

Value

A ggplot object, a scatter plot, demonstrating the relationship between scores from two signatures on the same set of samples.

Examples

ranked <- rankGenes(toy_expr_se) scoredf <- simpleScore(ranked, upSet = toy_gs_up, downSet = toy_gs_dn) scoredf2 <- simpleScore(ranked, upSet = toy_gs_up) plotScoreLandscape(scoredf, scoredf2)