tests/testthat/test_lhc_plotting.R

In kalden/spartan: Simulation Parameter Analysis R Toolkit ApplicatioN: 'spartan'

library(spartan)
context("Testing Spartan LHC Plotting Utilities Class")

test_that("lhc_graphMeasuresForParameterChange", {

  # Setup:
  load(file.path("LHC_Summary.Rda"))
  # Write to file so can be read in
  write.csv(LHCRESULTFILE,file="LHC_Results.csv",row.names=F,quote=F)
  # Load Correlation Coefficients
  load(file.path("test_cor_coeffs.Rda"))
  write.csv(test_cor_coeffs,file="Test_Cor_Coeffs.csv",row.names=F,quote=F)

  # All internals have been tested - we now need to check for output
  lhc_graphMeasuresForParameterChange(getwd(), c("thresholdBindProbability", "chemoThreshold", "chemoUpperLinearAdjust",
                                                 "chemoLowerLinearAdjust", "maxVCAMeffectProbabilityCutoff", "vcamSlope"),
                                      c("Velocity","Displacement"), c("microns/min","microns"), "Test_Cor_Coeffs.csv",
                                      "LHC_Results.csv", OUTPUT_TYPE = c("PDF","PNG"))

  # Check for existence of graphs
  expect_true(file.exists(file.path(getwd(),"thresholdBindProbability_Velocity.pdf")))
  expect_true(file.exists(file.path(getwd(),"chemoThreshold_Velocity.pdf")))
  expect_true(file.exists(file.path(getwd(),"chemoUpperLinearAdjust_Velocity.pdf")))
  expect_true(file.exists(file.path(getwd(),"chemoLowerLinearAdjust_Velocity.pdf")))
  expect_true(file.exists(file.path(getwd(),"maxVCAMeffectProbabilityCutoff_Velocity.pdf")))
  expect_true(file.exists(file.path(getwd(),"vcamSlope_Velocity.pdf")))
  expect_true(file.exists(file.path(getwd(),"thresholdBindProbability_Displacement.pdf")))
  expect_true(file.exists(file.path(getwd(),"chemoThreshold_Displacement.pdf")))
  expect_true(file.exists(file.path(getwd(),"chemoUpperLinearAdjust_Displacement.pdf")))
  expect_true(file.exists(file.path(getwd(),"chemoLowerLinearAdjust_Displacement.pdf")))
  expect_true(file.exists(file.path(getwd(),"maxVCAMeffectProbabilityCutoff_Displacement.pdf")))
  expect_true(file.exists(file.path(getwd(),"vcamSlope_Displacement.pdf")))

  expect_true(file.exists(file.path(getwd(),"thresholdBindProbability_Velocity.png")))
  expect_true(file.exists(file.path(getwd(),"chemoThreshold_Velocity.png")))
  expect_true(file.exists(file.path(getwd(),"chemoUpperLinearAdjust_Velocity.png")))
  expect_true(file.exists(file.path(getwd(),"chemoLowerLinearAdjust_Velocity.png")))
  expect_true(file.exists(file.path(getwd(),"maxVCAMeffectProbabilityCutoff_Velocity.png")))
  expect_true(file.exists(file.path(getwd(),"vcamSlope_Velocity.png")))
  expect_true(file.exists(file.path(getwd(),"thresholdBindProbability_Displacement.png")))
  expect_true(file.exists(file.path(getwd(),"chemoThreshold_Displacement.png")))
  expect_true(file.exists(file.path(getwd(),"chemoUpperLinearAdjust_Displacement.png")))
  expect_true(file.exists(file.path(getwd(),"chemoLowerLinearAdjust_Displacement.png")))
  expect_true(file.exists(file.path(getwd(),"maxVCAMeffectProbabilityCutoff_Displacement.png")))
  expect_true(file.exists(file.path(getwd(),"vcamSlope_Displacement.png")))


  file.remove("LHC_Results.csv")
  file.remove("Test_Cor_Coeffs.csv")
  file.remove("thresholdBindProbability_Velocity.pdf")
  file.remove("chemoThreshold_Velocity.pdf")
  file.remove("chemoUpperLinearAdjust_Velocity.pdf")
  file.remove("chemoLowerLinearAdjust_Velocity.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_Velocity.pdf")
  file.remove("vcamSlope_Velocity.pdf")
  file.remove("thresholdBindProbability_Displacement.pdf")
  file.remove("chemoThreshold_Displacement.pdf")
  file.remove("chemoUpperLinearAdjust_Displacement.pdf")
  file.remove("chemoLowerLinearAdjust_Displacement.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_Displacement.pdf")
  file.remove("vcamSlope_Displacement.pdf")

  file.remove("thresholdBindProbability_Velocity.png")
  file.remove("chemoThreshold_Velocity.png")
  file.remove("chemoUpperLinearAdjust_Velocity.png")
  file.remove("chemoLowerLinearAdjust_Velocity.png")
  file.remove("maxVCAMeffectProbabilityCutoff_Velocity.png")
  file.remove("vcamSlope_Velocity.png")
  file.remove("thresholdBindProbability_Displacement.png")
  file.remove("chemoThreshold_Displacement.png")
  file.remove("chemoUpperLinearAdjust_Displacement.png")
  file.remove("chemoLowerLinearAdjust_Displacement.png")
  file.remove("maxVCAMeffectProbabilityCutoff_Displacement.png")
  file.remove("vcamSlope_Displacement.png")

})

test_that("lhc_graphMeasuresForParameterChange_overTime", {

  # Setup:
  load(file.path("LHC_Summary.Rda"))
  load(file.path("LHC_Summary_36.Rda"))
  write.csv(LHCRESULTFILE,file="LHC_Results_12.csv",row.names=F,quote=F)
  write.csv(LHCRESULTFILE_36,file="LHC_Results_36.csv",row.names=F,quote=F)
  # Load Correlation Coefficients
  load(file.path("test_cor_coeffs.Rda"))
  load(file.path("test_cor_coeffs_36.Rda"))
  write.csv(test_cor_coeffs,file="Test_Cor_Coeffs_12.csv",row.names=F,quote=F)
  write.csv(test_cor_coeffs_36,file="Test_Cor_Coeffs_36.csv",row.names=F,quote=F)

  # All internals have been tested - we now need to check for output
  lhc_graphMeasuresForParameterChange(getwd(), c("thresholdBindProbability", "chemoThreshold", "chemoUpperLinearAdjust",
                                                 "chemoLowerLinearAdjust", "maxVCAMeffectProbabilityCutoff", "vcamSlope"),
                                      c("Velocity","Displacement"), c("microns/min","microns"), "Test_Cor_Coeffs.csv",
                                      "LHC_Results.csv", OUTPUT_TYPE = c("PDF","PNG"),TIMEPOINTS=c(12,36),TIMEPOINTSCALE="Hours")

  file.remove("LHC_Results_12.csv")
  file.remove("LHC_Results_36.csv")
  file.remove("Test_Cor_Coeffs_12.csv")
  file.remove("Test_Cor_Coeffs_36.csv")
  file.remove("thresholdBindProbability_Velocity_12.pdf")
  file.remove("chemoThreshold_Velocity_12.pdf")
  file.remove("chemoUpperLinearAdjust_Velocity_12.pdf")
  file.remove("chemoLowerLinearAdjust_Velocity_12.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_Velocity_12.pdf")
  file.remove("vcamSlope_Velocity_12.pdf")
  file.remove("thresholdBindProbability_Displacement_12.pdf")
  file.remove("chemoThreshold_Displacement_12.pdf")
  file.remove("chemoUpperLinearAdjust_Displacement_12.pdf")
  file.remove("chemoLowerLinearAdjust_Displacement_12.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_Displacement_12.pdf")
  file.remove("vcamSlope_Displacement_12.pdf")

  file.remove("thresholdBindProbability_Velocity_36.pdf")
  file.remove("chemoThreshold_Velocity_36.pdf")
  file.remove("chemoUpperLinearAdjust_Velocity_36.pdf")
  file.remove("chemoLowerLinearAdjust_Velocity_36.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_Velocity_36.pdf")
  file.remove("vcamSlope_Velocity_36.pdf")
  file.remove("thresholdBindProbability_Displacement_36.pdf")
  file.remove("chemoThreshold_Displacement_36.pdf")
  file.remove("chemoUpperLinearAdjust_Displacement_36.pdf")
  file.remove("chemoLowerLinearAdjust_Displacement_36.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_Displacement_36.pdf")
  file.remove("vcamSlope_Displacement_36.pdf")


})

test_that("make_graph_title", {

  graph_list <- make_graph_title(getwd(), "A", NULL, "Velocity",
                               "microns/min", 0.9, NULL)

  expect_true(length(graph_list)==5)
  expect_true(graph_list$title=="LHC Analysis for Parameter: A")
  expect_true(graph_list$file==file.path(getwd(),"A_Velocity"))
  expect_true(graph_list$sub_title=="Measure: Velocity\nCorrelation Coefficient: 0.9")
  expect_true(graph_list$xlabel == "Parameter Value")
  expect_true(graph_list$ylabel == "Median Value Across Runs (microns/min)")
})

test_that("lhc_netlogo_graphMeasuresForParameterChange", {
  expect_message(lhc_netlogo_graphMeasuresForParameterChange(getwd(), c("A","B"),c("R","W"),c("m","m"),"Co_File.csv","lhc_File.csv",NULL,NULL),"Deprecated. Use the lhc_graphMeasuresForParameterChange method instead")

})

test_that("plotPRCCSFromTimepointFiles", {

  # Again just testing we get some output from the plotting functions:
  load(file.path("test_cor_coeffs.Rda"))
  load(file.path("test_cor_coeffs_36.Rda"))
  write.csv(test_cor_coeffs,file="Test_Cor_Coeffs_12.csv",row.names=F,quote=F)
  write.csv(test_cor_coeffs_36,file="Test_Cor_Coeffs_36.csv",row.names=F,quote=F)


  plotPRCCSFromTimepointFiles(getwd(), c("thresholdBindProbability", "chemoThreshold", "chemoUpperLinearAdjust",
                                                     "chemoLowerLinearAdjust", "maxVCAMeffectProbabilityCutoff", "vcamSlope"),
                                          c("Velocity","Displacement"), "Test_Cor_Coeffs.csv", c(12,36),"Hours", DISPLAYPVALS = FALSE)

  # Check file existence
  expect_true(file.exists("thresholdBindProbability_OverTime.pdf"))
  expect_true(file.exists("chemoThreshold_OverTime.pdf"))
  expect_true(file.exists("chemoUpperLinearAdjust_OverTime.pdf"))
  expect_true(file.exists("chemoLowerLinearAdjust_OverTime.pdf"))
  expect_true(file.exists("maxVCAMeffectProbabilityCutoff_OverTime.pdf"))
  expect_true(file.exists("vcamSlope_OverTime.pdf"))

  file.remove("thresholdBindProbability_OverTime.pdf")
  file.remove("chemoThreshold_OverTime.pdf")
  file.remove("chemoUpperLinearAdjust_OverTime.pdf")
  file.remove("chemoLowerLinearAdjust_OverTime.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_OverTime.pdf")
  file.remove("vcamSlope_OverTime.pdf")

  plotPRCCSFromTimepointFiles(getwd(), c("thresholdBindProbability", "chemoThreshold", "chemoUpperLinearAdjust",
                                         "chemoLowerLinearAdjust", "maxVCAMeffectProbabilityCutoff", "vcamSlope"),
                              c("Velocity","Displacement"), "Test_Cor_Coeffs.csv", c(12,36),"Hours", DISPLAYPVALS = TRUE)

  expect_true(file.exists("thresholdBindProbability_OverTime.pdf"))
  expect_true(file.exists("chemoThreshold_OverTime.pdf"))
  expect_true(file.exists("chemoUpperLinearAdjust_OverTime.pdf"))
  expect_true(file.exists("chemoLowerLinearAdjust_OverTime.pdf"))
  expect_true(file.exists("maxVCAMeffectProbabilityCutoff_OverTime.pdf"))
  expect_true(file.exists("vcamSlope_OverTime.pdf"))

  file.remove("thresholdBindProbability_OverTime.pdf")
  file.remove("chemoThreshold_OverTime.pdf")
  file.remove("chemoUpperLinearAdjust_OverTime.pdf")
  file.remove("chemoLowerLinearAdjust_OverTime.pdf")
  file.remove("maxVCAMeffectProbabilityCutoff_OverTime.pdf")
  file.remove("vcamSlope_OverTime.pdf")
  file.remove("Test_Cor_Coeffs_12.csv")
  file.remove("Test_Cor_Coeffs_36.csv")

})

test_that("lhc_polarplot", {
  # Test graphic creation

  load(file.path("test_cor_coeffs.Rda"))
  write.csv(test_cor_coeffs,file="Test_Cor_Coeffs.csv",row.names=F,quote=F)

  lhc_polarplot(getwd(), c("thresholdBindProbability", "chemoThreshold", "chemoUpperLinearAdjust",
                           "chemoLowerLinearAdjust", "maxVCAMeffectProbabilityCutoff", "vcamSlope"),
                c("Velocity","Displacement"), "Test_Cor_Coeffs.csv",
                            TIMEPOINTS = NULL, TIMEPOINTSCALE = NULL)

  expect_true(file.exists("polarPlot_Velocity.pdf"))
  expect_true(file.exists("polarPlot_Velocity.png"))
  expect_true(file.exists("polarPlot_Displacement.pdf"))
  expect_true(file.exists("polarPlot_Displacement.png"))

  file.remove("polarPlot_Velocity.pdf")
  file.remove("polarPlot_Velocity.png")
  file.remove("polarPlot_Displacement.pdf")
  file.remove("polarPlot_Displacement.png")
  file.remove("Test_Cor_Coeffs.csv")

  # Timepoints:
  load(file.path("test_cor_coeffs.Rda"))
  load(file.path("test_cor_coeffs_36.Rda"))
  write.csv(test_cor_coeffs,file="Test_Cor_Coeffs_12.csv",row.names=F,quote=F)
  write.csv(test_cor_coeffs_36,file="Test_Cor_Coeffs_36.csv",row.names=F,quote=F)

  lhc_polarplot(getwd(), c("thresholdBindProbability", "chemoThreshold", "chemoUpperLinearAdjust",
                           "chemoLowerLinearAdjust", "maxVCAMeffectProbabilityCutoff", "vcamSlope"),
                c("Velocity","Displacement"), "Test_Cor_Coeffs.csv",
                TIMEPOINTS = c(12,36), TIMEPOINTSCALE = "Hours")

  expect_true(file.exists("polarPlot_Velocity_12.pdf"))
  expect_true(file.exists("polarPlot_Velocity_12.png"))
  expect_true(file.exists("polarPlot_Velocity_36.pdf"))
  expect_true(file.exists("polarPlot_Velocity_36.png"))
  expect_true(file.exists("polarPlot_Displacement_12.pdf"))
  expect_true(file.exists("polarPlot_Displacement_12.png"))
  expect_true(file.exists("polarPlot_Displacement_36.pdf"))
  expect_true(file.exists("polarPlot_Displacement_36.png"))

  file.remove("polarPlot_Velocity_12.pdf")
  file.remove("polarPlot_Velocity_12.png")
  file.remove("polarPlot_Velocity_36.pdf")
  file.remove("polarPlot_Velocity_36.png")
  file.remove("polarPlot_Displacement_12.pdf")
  file.remove("polarPlot_Displacement_12.png")
  file.remove("polarPlot_Displacement_36.pdf")
  file.remove("polarPlot_Displacement_36.png")
  file.remove("Test_Cor_Coeffs_12.csv")
  file.remove("Test_Cor_Coeffs_36.csv")

})

test_that("lhc_plotCoEfficients", {

  dir.create("graph_area")
  load(file.path("test_cor_coeffs.Rda"))
  write.csv(test_cor_coeffs,file="graph_area/Test_Cor_Coeffs.csv",row.names=F,quote=F)

  lhc_plotCoEfficients(paste(getwd(),"/graph_area",sep=""), "Test_Cor_Coeffs.csv", c("Velocity","Displacement"),
                       "ALL")

  expect_true(file.exists("graph_area/PRCC_AllMeasures.pdf"))

  lhc_plotCoEfficients(paste(getwd(),"/graph_area",sep=""), "Test_Cor_Coeffs.csv", c("Velocity","Displacement"),
                       "INDIVIDUAL")

  expect_true(file.exists("graph_area/PRCC_Measure_Displacement.pdf"))
  expect_true(file.exists("graph_area/PRCC_Measure_Velocity.pdf"))

  # Over time:
  load(file.path("test_cor_coeffs.Rda"))
  load(file.path("test_cor_coeffs_36.Rda"))
  write.csv(test_cor_coeffs,file="graph_area/Test_Cor_Coeffs_12.csv",row.names=F,quote=F)
  write.csv(test_cor_coeffs_36,file="graph_area/Test_Cor_Coeffs_36.csv",row.names=F,quote=F)

  lhc_plotCoEfficients(paste(getwd(),"/graph_area",sep=""), "Test_Cor_Coeffs.csv", c("Velocity","Displacement"),
                       "ALL",TIMEPOINTS=c(12,36),TIMEPOINTSCALE="Hours")

  lhc_plotCoEfficients(paste(getwd(),"/graph_area",sep=""), "Test_Cor_Coeffs.csv", c("Velocity","Displacement"),
                       "INDIVIDUAL",TIMEPOINTS=c(12,36),TIMEPOINTSCALE="Hours")

  expect_true(file.exists("graph_area/PRCC_AllMeasures_12.pdf"))
  expect_true(file.exists("graph_area/PRCC_AllMeasures_36.pdf"))
  expect_true(file.exists("graph_area/PRCC_Measure_Displacement_12.pdf"))
  expect_true(file.exists("graph_area/PRCC_Measure_Displacement_36.pdf"))
  expect_true(file.exists("graph_area/PRCC_Measure_Velocity_12.pdf"))
  expect_true(file.exists("graph_area/PRCC_Measure_Velocity_36.pdf"))

  unlink("graph_area",recursive = TRUE)

})