plotsome: Various types of plots of Equitable transform data dependent...

In celphin/Equitable: Equitable Transform

Various types of plots of Equitable transform data dependent on options chosen

Description

Uses functions plotimages plotindiv plotO_S_E_lscol plotversus plot_vsref. The function plotsummary uses this function to summarize the transform data

Usage

plotsome(
  T,
  num = 5,
  signal = NULL,
  limits = NULL,
  xlimits = NULL,
  indiv = FALSE,
  columns = FALSE,
  images = TRUE,
  density = FALSE,
  versus = FALSE,
  xvsref = NULL,
  yline = 3,
  yma = 5,
  transpose = FALSE,
  of = FALSE,
  lf = FALSE,
  ef = TRUE,
  avef = FALSE,
  errb = FALSE,
  row_unit = NULL,
  col_unit = NULL,
  z_unit = NULL,
  genname = NULL,
  stderror = FALSE,
  fcontour = TRUE
)

Arguments

T	equitable transform info: output from transformE
num	5 default number of indiviual plot to be made
signal	2D data set representing the signal. Must be the same size as T$smat
limits	default NULL limits on yaxis of plots and range for rainbow colouring in images
xlimits	default NULL limits on xaxis of plots
indiv	default FALSE: plots individual row or column dependendent on transpose flag
columns	default FALSE TRUE:plot all columns on one plot
images	default TRUE: plots false colour images
density	ignore
versus	plots all individual vs reference default FALSE:
xvsref	column to be used as reference against which all others are plotted default NULL
yline	default 3 lines out from plot to display yaxis values
yma	default 5 cahracters out from plot to display ylabel
transpose	default FALSE TRUE: plot all rows on one plot
of	according to above flags plots original data default FALSE
lf	according to above flags plots least squares transformdata default FALSE
ef	according to above flags plots equitable transform data default FALSE
avef	according to above flags plots equitbale transform data formed using only average profile default FALSE
errb	according to above flags uses error bars when possible default FALSE
row_unit	row axis label default Row Number
col_unit	column axis label default Row Number
z_unit	label for quantity measured in data
genname	main title to be included
stderror	according to above flags uses error bars of standard error rather than standard deviaiton when possible default FALSE
fcontour	default TRUE: plots contour maps

Value

None

Examples

d<-eg4(2,2)
Td<-transformE(d)
d_noise<-d+rnorm(prod(dim(d)),mean=0,sd=(1/4*sd(d,na.rm=TRUE)))
Td_noise<-transformE(d_noise)
plotsome(T=Td_noise,lf=TRUE,of=TRUE)
# default only plots imagef of signal original and equitable
plotsome(T=Td_noise,signal=Td$smat,of=TRUE)
plotsome(T=Td_noise,signal=Td$smat,indiv=TRUE,xvsref=ncol(Td$smat))
plotsome(T=Td_noise,signal=Td$smat,columns=TRUE,images=FALSE,
lf=TRUE,of=TRUE)
plotsome(T=Td_noise,signal=Td$smat,columns=TRUE,images=FALSE,
transpose=TRUE,lf=TRUE,of=TRUE)
plotsome(T=Td_noise,signal=Td$smat,indiv=TRUE,of=TRUE,lf=TRUE)
plotsome(T=Td_noise,signal=Td$smat,indiv=TRUE,of=TRUE,errb=TRUE)
plotsome(T=Td_noise,signal=Td$smat,indiv=TRUE,of=TRUE,errb=TRUE,stderror=TRUE)
#num= NULL  all individuals are plotted
plotsome(T=Td_noise,signal=Td$smat,indiv=TRUE,of=TRUE,num=NULL)
# plots images and transforms vs original and signal
plotsome(T=Td_noise,signal=Td$smat,of=TRUE,lf=TRUE,versus=TRUE)

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