plot.TendrilPerm: Plot TendrilPerm

Description Usage Arguments Examples

View source: R/plot.TendrilPerm.R

Description

Function to plot TendrilPerm results

Usage

1
2
3
## S3 method for class 'TendrilPerm'
plot(x, coloring = "p.adj", percentile = FALSE,
  ...)

Arguments

x

An object of class TendrilPerm, as made by TendrilPerm()

coloring

Name of column used for coloring tendrils. Available coloring choices are: "Terms" - One tendril one color; "p" - Prop.test; "p.adj" - P-values adjusted using the False discovery rate method within each tendril; "fish" - Fisher.test; "rdiff" - Risk difference; "RR" - Risk Ratio; "OR" - Odds Ratio; "FDR.tot" - P-values adjusted using the False discovery rate method for all tendrils; and "TermsCount" - Total number of events for that specific type of event

percentile

Specifies if the plot must show percentile values. Default is FALSE.

...

unused

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
# generate data using Tendril()
data <- Tendril(mydata = TendrilData,
rotations = Rotations,
AEfreqThreshold = 9,
Tag = "Comment",
Treatments = c("placebo", "active"),
Unique.Subject.Identifier = "subjid",
Terms = "ae",
Treat = "treatment",
StartDay = "day",
SubjList = SubjList,
SubjList.subject = "subjid",
SubjList.treatment = "treatment"
)
tendril_perm <- TendrilPerm(
  tendril = data,
  PermTerm="AE40",
  n.perm = 200,
  perm.from.day = 1)

#Do plot
res <- plot(tendril_perm)
res <- plot(tendril_perm, percentile = TRUE)

#To re-do the plot after the first call:
print(res)

Karpefors/Tendril documentation built on Jan. 17, 2020, 1:50 a.m.