tests/by_hand_tests/test_trelliscope.R

In EMSL-Computing/fticRanalysis: Analysis and visualization tools for FT-MS data

## Tests of creating trelliscope displays with the convenience functions in ftmsRanalysis

library(ftmsRanalysis)
library(trelliscope)

vdbDir <- vdbConn(file.path(tempdir(), "trell_test"), autoYes = TRUE)

data('exampleProcessedPeakData')

##########################################################
## SAMPLE PLOTS

sampleDdo <- divideBySample(exampleProcessedPeakData)

## TEST S-1: VK plot, color by VK category
panelFnS1 <- panelFunctionGenerator("vanKrevelenPlot", vkBoundarySet="bs2", title="Test")

makeDisplay(sampleDdo, 
            panelFn=panelFnS1,
            cogFn=vanKrevelenCognostics(vkBoundarySet="bs2"),
            name = "Trelliscope test S_1 with VK",
            group = "Sample")


## TEST S-2: Kendrick plot, color by VK category
panelFnS2 <- panelFunctionGenerator("kendrickPlot", vkBoundarySet="bs1")

makeDisplay(sampleDdo, 
            panelFn=panelFnS2,
            cogFn=kendrickCognostics(vkBoundarySet="bs1"),
            name = "Trelliscope test S_2 with Kendrick",
            group = "Sample")


## TEST S-3: VK plot, color by Intensity
panelFnS3 <- panelFunctionGenerator("vanKrevelenPlot", colorCName="Intensity")

makeDisplay(sampleDdo, 
            panelFn=panelFnS3,
            cogFn=vanKrevelenCognostics(),
            name = "Trelliscope test S_3 with VK",
            group = "Sample")


## TEST S-4: densityPlot of NOSC
panelFn4 <- panelFunctionGenerator("densityPlot", variable="NOSC")
makeDisplay(sampleDdo, 
            panelFn=panelFn4,
            cogFn=densityCognostics("NOSC"),
            name = "Trelliscope test S_4 with density",
            group = "Sample")

##########################################################
## GROUP PLOTS

groupDdo <- divideByGroup(exampleProcessedPeakData)
groupSummaryDdo <- summarizeGroups(groupDdo, summary_functions = c("prop_present", "n_present"))

## TEST G-1: VK group plot, color by proportion present
panelFnG1 <- panelFunctionGenerator("vanKrevelenPlot", colorCName=expr(paste0(getSplitVar(v, "Group"), "_prop_present")), 
                                   legendTitle="Proportion<br>Present")

makeDisplay(groupSummaryDdo, 
            panelFn=panelFnG1,
            cogFn=vanKrevelenCognostics(),
            name = "Trelliscope test G_1 with VK plot per group",
            group = "Group")


## TEST G-2: Kendrick group plot, color by n present
panelFnG2 <- panelFunctionGenerator("kendrickPlot", colorCName=expr(paste0(getSplitVar(v, "Group"), "_n_present")), 
                                   legendTitle="Number<br>Present")

makeDisplay(groupSummaryDdo, 
            panelFn=panelFnG2,
            cogFn=kendrickCognostics(),
            name = "Trelliscope test G_2 with Kendrick plot per group",
            group = "Group")



## TEST G-3: classes plot for each group
panelFnG3 <- panelFunctionGenerator("classesPlot")

makeDisplay(groupDdo, 
            panelFn=panelFnG3,
            name = "Trelliscope test G_3 with classesPlot",
            group = "Group")


## TEST G-4: density plot for each group
panelFnG4 <- panelFunctionGenerator("densityPlot", variable="NOSC", groups=NA)

makeDisplay(groupDdo, 
            panelFn=panelFnG4,
            cogFn=densityCognostics("NOSC"),
            name = "Trelliscope test G_4 with densityPlot",
            group = "Group")

view()


##########################################################
## GROUP COMPARISON PLOTS

exampleProcessedPeakData <- assign_class(exampleProcessedPeakData, "bs1")
grpCompDdo <- divideByGroupComparisons(exampleProcessedPeakData, "all")
grpCompSummaryDdo <- summarizeGroupComparisons(grpCompDdo, summary_functions="uniqueness_gtest", 
                                               summary_function_params=list(uniqueness_gtest=list(pres_fn="nsamps", pres_thresh=2, pvalue_thresh=0.05)))

## TEST GC-1: VK group comparison plot
panelFnGC1 <- panelFunctionGenerator("vanKrevelenPlot", colorCName="uniqueness_gtest")

makeDisplay(grpCompSummaryDdo, 
            panelFn=panelFnGC1,
            cogFn=vanKrevelenCognostics(),
            name = "Trelliscope test GC_1 with VK group comparison",
            group = "Group_Comparison")


## TEST GC-2: Kendrick group comparison plot
panelFnGC2 <- panelFunctionGenerator("kendrickPlot", colorCName="uniqueness_gtest")

makeDisplay(grpCompSummaryDdo, 
            panelFn=panelFnGC2,
            cogFn=kendrickCognostics(),
            name = "Trelliscope test GC_2 with Kendrick group comparison",
            group = "Group_Comparison")

## TEST GC-3: Density group comparison plot
panelFnGC3 <- panelFunctionGenerator("densityPlot", variable="NOSC", samples=FALSE, groups=NA)

makeDisplay(grpCompDdo, 
            panelFn=panelFnGC3,
            cogFn=densityCognostics("NOSC"),
            name = "Trelliscope test GC_3 with density on group comparison",
            group = "Group_Comparison")