gtoxPlotM4ID: Plot fit summary plot by m4id

In pmpsa-hpc/GladiaTOX: R Package for Processing High Content Screening data

Plot fit summary plot by m4id

Description

gtoxPlotM4ID creates a summary plots for the given m4id(s) by loading the appropriate data from the gtox databases and sending it to gtoxPlotFits

Usage

gtoxPlotM4ID(m4id, lvl = 4L, bline = "bmad")

Arguments

m4id	Integer, m4id(s) to plot
lvl	Integer, the level of data to plot
bline	Character of length 1, the value used for drawing the baseline noise

Details

A level 4 plot ('lvl' = 4) will plot the concentration series and the applicable curves, without an indication of the activity call or the winning model. Level 4 plots can be created without having done subsequent processing.

Level 5 plots include the level 4 information with the activity call and model selection. The winning model will be highlighted red in the side panel containing the summary statistics. Level 6 plots, in addition the all of the level 4 and 5 information, include the positive flag IDs. If the flag has an associated value, the value will be in parentheses follwing the flag ID.

Any values for 'bline' other than 'coff' will use 3*bmad.

Value

None

See Also

gtoxPlotFits, gtoxMakeAeidPlts

Examples

## Store the current config settings, so they can be reloaded at the end
## of the examples
conf_store <- gtoxConfList()
gtoxConfDefault()

acnm <- "Cytotoxicity (TIER1)_Cytochrome C release_24h"
pltnm <- "S-000049119"
myaid <- gtoxLoadApid()[u_boxtrack == pltnm, aid]
myaid <- myaid[myaid%in%gtoxLoadAid(fld = "asid", val = 1L)$aid]
apid <- gtoxLoadApid()[u_boxtrack == pltnm & aid == myaid, apid]
acid <- gtoxLoadAcid(fld = c("aid", "acnm"), val = list(myaid, acnm))[, acid]

aeid = gtoxLoadAeid(fld = c("acid", "analysis_direction"), 
  val = list(acid, "up"))[,aeid]
spid = gtoxLoadWaid(fld = c("apid", "wllt"), 
  val = list(apid, "c"))[,unique(spid)]
m4id = gtoxLoadData(lvl = 4L, fld = c("spid", "aeid"), 
  val = list(spid, aeid))[, m4id]

gtoxPlotM4ID(m4id = m4id, lvl = 6, bline = "coff") ## Create a level 4 plot
gtoxPlotM4ID(m4id = m4id, lvl = 5) ## Create a level 5 plot
gtoxPlotM4ID(m4id = m4id, lvl = 6) ## Create a level 6 plot

## Reset configuration
options(conf_store)

pmpsa-hpc/GladiaTOX documentation built on Sept. 1, 2023, 5:52 p.m.