NMTox (version 0.1.0)

nmplot.cat: Create plots of the dose and the response grouped by a variable

Description

This function generates scatter plots of the dose and the response, with the colour of the data points differentiated according to the value of a variable.

Usage

nmplot.cat(data.nm, data.control, id, nano, response, dose, end,
  end.cat, unit, unit.cat, x.cat, type = c("dose", "log"), control.opt =
  c("same", "all"), vars, nrow = 1, ncol = 1)

Value

This function produces scatter plots of the dose and the response, grouped by a certain variable

Arguments

data.nm

Data containing the result of toxicity study

data.control

Data of control values

id

Identifier of the experiment

nano

Name of the nanomaterial

response

Response (endpoint value)

dose

Dose or concentration

end

Toxicity endpoint

end.cat

Specific toxicity endpoint of interest

unit

Unit of measurement of the dose

unit.cat

Specific unit of measurement of the dose

x.cat

Variable used to differentiate the colour of the data points in the plot(s)

type

Type of the dose to be plotted ("dose" for dose and "log" for log(dose))

control.opt

Option for the control doses if unit and unit.cat are specified. If only control doses with the same unit of measurement as the non-control ones are included, then specify "same" in the control.opt. If all control doses with any units of measurement are included, then specify "all".

vars

Variable(s) used to subset the data

nrow

Number of rows in the plotting space (default is 1)

ncol

Number of columns in the plotting space (default is 1)

Details

• This function generates plots for each nanomaterial in the dataset (or for each subset of data). The different types of nanomaterials are identified by their names. Therefore, if some control values are named differently (see: geninvitro dataset and the Examples), a separate dataset containing only these values first needs to be created. Controls in the new dataset can be linked to the non-control observations belonging to the same experiment through the identifier of the experiment (the linking is performed inside this function). In this situation, it is necessary to have an indicator that can identify different experiments (such as experiment ID).

• If all controls in the dataset are named according to the related nanomaterial names, data.control and id do not need to be specified.

• If doses used in the experiment are all measured in the same unit of measurement, then specify "same" in control.opt.

• Dose-response plot can also be generated for subsets of data in each nanomaterial by specifying the variables used to split the data in vars.

Examples

# Example 1:
# Create a dataset containing controls (which are named differently)
# from geninvitro dataset:
controldata<-SubsetData(data=geninvitro, x="name", x.cat=c("control", "Control",
             "medium", "medium + BSA", "untreated"))

# Exclude controls (which are named differently) from geninvitro dataset:
invitrodata<-SubsetData(data=geninvitro, x="name", x.cat=c("control", "Control",
             "medium", "medium + BSA", "untreated"), include=FALSE)

# Generate dose-response plots for geninvitro, with DNA STRAND BREAKS as
# the endpoint, concentrations measured in "ug/cm2" and control doses
# measured in any units of measurement (different colours represent different
# study providers):
#
nmplot.cat(data.nm=invitrodata, data.control=controldata, id="experimentID",
           nano="name", response="value", dose="concentration", end="endpoint",
           end.cat="DNA STRAND BREAKS", unit="concentration_unit", unit.cat="ug/cm2",
           x.cat="studyprovider", type="dose", control.opt="all",
           nrow=1, ncol=1)

# Example 2:
# Split geninvitro data according to the method, study provider and unit of
# the concentration, and generate dose-response plot for each subset of data
# with DNA STRAND BREAKS as the endpoint (different colours represent
# different cell types):
#
nmplot.cat(data.nm=invitrodata, data.control=controldata, id="experimentID",
           nano="name", response="value", dose="concentration", end="endpoint",
           end.cat="DNA STRAND BREAKS",  x.cat="celltype", type="dose",
           vars=c("method","studyprovider","concentration_unit"),
           nrow=2, ncol=2)