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)
