xvsrefplot: Plots individual sequences against a reference sequence

In celphin/Equitable: Equitable Transform

Plots individual sequences against a reference sequence

Description

Equitable transform with errors, original and Equitable transform line parameters can be shown If number of point in variable t is less than 26 then each t point is colured and labelled in the legend

Usage

xvsrefplot(
  Td,
  cgroup = NULL,
  ylim = NULL,
  ref = NULL,
  br = "",
  pf = TRUE,
  extranames = NULL,
  err95 = TRUE,
  fitl = TRUE
)

Arguments

Td	transform information from transformE
cgroup	cgroup is the vector of columns to be plotted. Default NULL;10 colums across matrix are plotted
ylim	vector of min and max for plots to display default (NULL) function calculates same for all
ref	reference column against which all columns are plotted. Default NULL; column index with largest variation
br	text for headings of plots
pf	plotflag default TRUE
extranames	extra names to use for legend of t points
err95	2*std. dev/sqrt(N) where std deviation on the slope is found when calculating equitable slopes Default=TRUE
fitl	Default TRUE. Fitted line is displayed

Value

column index with largest variation amongst columns that were plotted

Examples

#first construct transfor of data and transform of signal
d<-eg4(1,2)
d_noise<-d+rnorm(prod(dim(d)),mean=0,sd=(1/4*sd(d,na.rm=TRUE)))
Td_noise<-transformE(d_noise)
xvsrefplot(Td=Td_noise)
xvsrefplot(Td=Td_noise,ref="Row_Ave")
nc<-seq(1,ncol(Td_noise$smat), by=1)
xvsrefplot(Td=Td_noise,cgroup=nc,ref=ncol(Td_noise$smat),
br=paste0( "Equitable Profiles"))
xvsrefplot(Td=Td_noise,cgroup=c(1,4,9,12),ref=7,
br=paste0( "Equitable Profiles"))
xvsrefplot(Td=Td_noise,cgroup=c(1,4,9,12),ref=7,
br=paste0( "Equitable Profiles with std dev"),fitl=FALSE)
xvsrefplot(Td=Td_noise,cgroup=c(12),ref=7,
br=paste0( "Equitable Profiles"))
xvsrefplot(Td=Td_noise,cgroup=c(12),ref=7,
br=paste0( "Equitable Profiles"),err95=FALSE)

d<-eg5(3,3)
d_noise<-d+rnorm(prod(dim(d)),mean=0,sd=(1/2*sd(d,na.rm=TRUE)))
Td_noise<-transformE(d_noise)
xvsrefplot(Td=Td_noise)

celphin/Equitable documentation built on Jan. 23, 2023, 11:02 p.m.