HitEnrichDiff {chemmodlab} | R Documentation |
Plot differences between hit enrichment curves
Description
Plot differences between hit enrichment curves based on scores from multiple algorithms. Actual activities are required. Additionally plot simultaneous confidence bands for these differences. Plots may be used to determine if one algorithm is "better" than another algorithm.
Usage
HitEnrichDiff(
S.df,
labels = NULL,
y,
x.max = NULL,
log = TRUE,
title = "",
conf.level = 0.95,
method = "sup-t",
plus = TRUE,
band.frac = NULL,
yrange = NULL
)
Arguments
S.df |
Data frame where variables are numeric scores from at least 2 different algorithms. Rows represent unique compounds. |
labels |
Character vector of labels for the different algorithms in
|
y |
Numeric vector of activity values. Activity values must be either 0
(inactive/undesirable) or 1 (active/desirable); no other values are
accepted. Compounds are assumed to be in the same order as in |
x.max |
Integer, the maximum number of tests allowed on the x axis. |
log |
Logical. |
title |
Character string |
conf.level |
Numeric, confidence coefficient |
method |
Character indicates the method used to obtain confidence bands.
The default is |
plus |
Logical. |
band.frac |
Numeric vector of fractions tested to be used in obtaining
confidence bands. Vector should be no longer than |
yrange |
Numeric vector of length 2. The desired range for the y axis. |
Details
By default, x.max
is length(y)
, so that hit enrichment
curves are obtained for all observable fractions, i.e., fractions of
(1:length(y))/length(y)
. By default, confidence bands are evaluated
based on a smaller grid of 40 fractions. This smaller grid is evenly spaced
on either the original grid of (1:length(y))/length(y)
, or the log
scale of the original grid.