ds.contourPlot: Generates a contour plot

In datashield/dsBaseClient: DataSHIELD Client Functions

Generates a contour plot

Description

It generates a contour plot of the pooled data or one plot for each dataset on the client-side.

Usage

ds.contourPlot(
  x = NULL,
  y = NULL,
  type = "combine",
  show = "all",
  numints = 20,
  method = "smallCellsRule",
  k = 3,
  noise = 0.25,
  datasources = NULL
)

Arguments

x	a character string providing the name of a numerical vector.
y	a character string providing the name of a numerical vector.
type	a character string that represents the type of graph to display. If type is set to 'combine', a combined contour plot displayed and if type is set to 'split', each contour is plotted separately.
show	a character that represents where the plot should focus. If show is set to 'all', the ranges of the variables are used as plot limits. If show is set to 'zoomed', the plot is zoomed to the region where the actual data are.
numints	number of intervals for a density grid object.
method	a character that defines which contour will be created. If method is set to 'smallCellsRule' (default), the contour plot of the actual variables is created but grids with low counts are replaced with grids with zero counts. If method is set to 'deterministic' the contour of the scaled centroids of each k nearest neighbour of the original variables is created, where the value of k is set by the user. If the method is set to 'probabilistic', then the contour of 'noisy' variables is generated.
k	the number of the nearest neighbours for which their centroid is calculated. For more information see details.
noise	the percentage of the initial variance that is used as the variance of the embedded noise if the argument method is set to 'probabilistic'. For more information see details.
datasources	a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Details

The ds.contourPlot function first generates a density grid and uses it to plot the graph. The cells of the grid density matrix that hold a count of less than the filter set by DataSHIELD (usually 5) are considered invalid and turned into 0 to avoid potential disclosure. A message is printed to inform the user about the number of invalid cells.

The ranges returned by each study and used in the process of getting the grid density matrix are not the exact minimum and maximum values but rather close approximates of the real minimum and maximum value. This was done to reduce the risk of potential disclosure.

In the k parameter the user can choose any value for k equal to or greater than the pre-specified threshold used as a disclosure control for this method and lower than the number of observations minus the value of this threshold. k default value is 3 (we suggest k to be equal to, or bigger than, 3). Note that the function fails if the user uses the default value but the study has set a bigger threshold. The value of k is used only if the argument method is set to 'deterministic'. Any value of k is ignored if the argument method is set to 'probabilistic' or 'smallCellsRule'.

In noise any value of noise is ignored if the argument method is set to 'deterministic' or 'smallCellsRule'. The user can choose any value for noise equal to or greater than the pre-specified threshold 'nfilter.noise'. Default noise value is 0.25. The added noise follows a normal distribution with zero mean and variance equal to a percentage of the initial variance of each input variable.

Server functions called: heatmapPlotDS, rangeDS and densityGridDS

Value

ds.contourPlot returns a contour plot to the client-side.

Author(s)

DataSHIELD Development Team

Examples

## Not run: 

  ## Version 6, for version 5 see the Wiki
  # Connecting to the Opal servers

  require('DSI')
  require('DSOpal')
  require('dsBaseClient')

  builder <- DSI::newDSLoginBuilder()
  builder$append(server = "study1", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "CNSIM.CNSIM1", driver = "OpalDriver")
  builder$append(server = "study2", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "CNSIM.CNSIM2", driver = "OpalDriver")
  builder$append(server = "study3",
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "CNSIM.CNSIM3", driver = "OpalDriver")
  logindata <- builder$build()
  
  # Log onto the remote Opal training servers
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # Generating contour plots

  ds.contourPlot(x = "D$LAB_TSC",
                 y = "D$LAB_HDL",
                 type = "combine", 
                 show = "all",
                 numints = 20,
                 method = "smallCellsRule",  
                 k = 3, 
                 noise = 0.25,
                 datasources = connections)

  # clear the Datashield R sessions and logout
  datashield.logout(connections)


## End(Not run)

datashield/dsBaseClient documentation built on Nov. 16, 2024, 2:07 p.m.