Make sure to be familiar with the following tutorials before proceeding:
The number of data variables that can result from high throughput microscopy experiments is vast. The examples we use throughout our tutorials often contain more than 300 of them. In order to keep track and do proper, convenient analysis we implemented a concept called Variable Sets. Variable sets are predefined sets of variable names gathered under a specific name. This, for one thing, facilitates analysis as it often saves a lot of manual typing. Additionally, it helps to keep track of the different perspectives from which you can analyze cells as well as it helps to compare the results.
Let’s assume that the current question at hand is all around the cells shape and variables regarding intensity, granularity etc. are not of interest.
all_var_names <- getStatVariableNames(object)
all_var_namesoutput
## [1] "x_coords"
## [2] "y_coords"
## [3] "frame_num"
## [4] "AreaShape_Area"
## [5] "AreaShape_BoundingBoxArea"
## [6] "AreaShape_BoundingBoxMaximum_X"
## [7] "AreaShape_BoundingBoxMaximum_Y"
## [8] "AreaShape_BoundingBoxMinimum_X"
## [9] "AreaShape_BoundingBoxMinimum_Y"
## [10] "AreaShape_Center_X"
## [11] "AreaShape_Center_Y"
## [12] "AreaShape_Compactness"
## [13] "AreaShape_Eccentricity"
## [14] "AreaShape_EquivalentDiameter"
## [15] "AreaShape_EulerNumber"
## [16] "AreaShape_Extent"
## [17] "AreaShape_FormFactor"
## [18] "AreaShape_MajorAxisLength"
## [19] "AreaShape_MaxFeretDiameter"
## [20] "AreaShape_MaximumRadius"
## [21] "AreaShape_MeanRadius"
## [22] "AreaShape_MedianRadius"
## [23] "AreaShape_MinFeretDiameter"
## [24] "AreaShape_MinorAxisLength"
## [25] "AreaShape_Orientation"
## [26] "AreaShape_Perimeter"
## [27] "AreaShape_Solidity"
## [28] "AreaShape_Zernike_0_0"
## [29] "AreaShape_Zernike_1_1"
## [30] "AreaShape_Zernike_2_0"
## [31] "AreaShape_Zernike_2_2"
## [32] "AreaShape_Zernike_3_1"
## [33] "AreaShape_Zernike_3_3"
## [34] "AreaShape_Zernike_4_0"
## [35] "AreaShape_Zernike_4_2"
## [36] "AreaShape_Zernike_4_4"
## [37] "AreaShape_Zernike_5_1"
## [38] "AreaShape_Zernike_5_3"
## [39] "AreaShape_Zernike_5_5"
## [40] "AreaShape_Zernike_6_0"
## [41] "AreaShape_Zernike_6_2"
## [42] "AreaShape_Zernike_6_4"
## [43] "AreaShape_Zernike_6_6"
## [44] "AreaShape_Zernike_7_1"
## [45] "AreaShape_Zernike_7_3"
## [46] "AreaShape_Zernike_7_5"
## [47] "AreaShape_Zernike_7_7"
## [48] "AreaShape_Zernike_8_0"
## [49] "AreaShape_Zernike_8_2"
## [50] "AreaShape_Zernike_8_4"
## [51] "AreaShape_Zernike_8_6"
## [52] "AreaShape_Zernike_8_8"
## [53] "AreaShape_Zernike_9_1"
## [54] "AreaShape_Zernike_9_3"
## [55] "AreaShape_Zernike_9_5"
## [56] "AreaShape_Zernike_9_7"
## [57] "AreaShape_Zernike_9_9"
## [58] "Children_Cytoplasm_Count"
## [59] "Granularity_10_Actin"
## [60] "Granularity_11_Actin"
## [61] "Granularity_12_Actin"
## [62] "Granularity_13_Actin"
## [63] "Granularity_14_Actin"
## [64] "Granularity_15_Actin"
## [65] "Granularity_16_Actin"
## [66] "Granularity_1_Actin"
## [67] "Granularity_2_Actin"
## [68] "Granularity_3_Actin"
## [69] "Granularity_4_Actin"
## [70] "Granularity_5_Actin"
## [71] "Granularity_6_Actin"
## [72] "Granularity_7_Actin"
## [73] "Granularity_8_Actin"
## [74] "Granularity_9_Actin"
## [75] "Intensity_IntegratedIntensityEdge_Actin"
## [76] "Intensity_IntegratedIntensity_Actin"
## [77] "Intensity_LowerQuartileIntensity_Actin"
## [78] "Intensity_MADIntensity_Actin"
## [79] "Intensity_MassDisplacement_Actin"
## [80] "Intensity_MaxIntensityEdge_Actin"
## [81] "Intensity_MaxIntensity_Actin"
## [82] "Intensity_MeanIntensityEdge_Actin"
## [83] "Intensity_MeanIntensity_Actin"
## [84] "Intensity_MedianIntensity_Actin"
## [85] "Intensity_MinIntensityEdge_Actin"
## [86] "Intensity_MinIntensity_Actin"
## [87] "Intensity_StdIntensityEdge_Actin"
## [88] "Intensity_StdIntensity_Actin"
## [89] "Intensity_UpperQuartileIntensity_Actin"
## [90] "Location_CenterMassIntensity_X_Actin"
## [91] "Location_CenterMassIntensity_Y_Actin"
## [92] "Location_MaxIntensity_X_Actin"
## [93] "Location_MaxIntensity_Y_Actin"
## [94] "Neighbors_AngleBetweenNeighbors_10"
## [95] "Neighbors_AngleBetweenNeighbors_Adjacent"
## [96] "Neighbors_FirstClosestDistance_10"
## [97] "Neighbors_FirstClosestDistance_Adjacent"
## [98] "Neighbors_FirstClosestObjectNumber_10"
## [99] "Neighbors_FirstClosestObjectNumber_Adjacent"
## [100] "Neighbors_NumberOfNeighbors_10"
## [101] "Neighbors_NumberOfNeighbors_Adjacent"
## [102] "Neighbors_PercentTouching_10"
## [103] "Neighbors_PercentTouching_Adjacent"
## [104] "Neighbors_SecondClosestDistance_10"
## [105] "Neighbors_SecondClosestDistance_Adjacent"
## [106] "Neighbors_SecondClosestObjectNumber_10"
## [107] "Neighbors_SecondClosestObjectNumber_Adjacent"
## [108] "Number_Object_Number"
## [109] "Parent_Nuclei"
## [110] "RadialDistribution_FracAtD_Actin_1of4"
## [111] "RadialDistribution_FracAtD_Actin_2of4"
## [112] "RadialDistribution_FracAtD_Actin_3of4"
## [113] "RadialDistribution_FracAtD_Actin_4of4"
## [114] "RadialDistribution_MeanFrac_Actin_1of4"
## [115] "RadialDistribution_MeanFrac_Actin_2of4"
## [116] "RadialDistribution_MeanFrac_Actin_3of4"
## [117] "RadialDistribution_MeanFrac_Actin_4of4"
## [118] "RadialDistribution_RadialCV_Actin_1of4"
## [119] "RadialDistribution_RadialCV_Actin_2of4"
## [120] "RadialDistribution_RadialCV_Actin_3of4"
## [121] "RadialDistribution_RadialCV_Actin_4of4"
## [122] "RadialDistribution_ZernikeMagnitude_Actin_0_0"
## [123] "RadialDistribution_ZernikeMagnitude_Actin_1_1"
## [124] "RadialDistribution_ZernikeMagnitude_Actin_2_0"
## [125] "RadialDistribution_ZernikeMagnitude_Actin_2_2"
## [126] "RadialDistribution_ZernikeMagnitude_Actin_3_1"
## [127] "RadialDistribution_ZernikeMagnitude_Actin_3_3"
## [128] "RadialDistribution_ZernikeMagnitude_Actin_4_0"
## [129] "RadialDistribution_ZernikeMagnitude_Actin_4_2"
## [130] "RadialDistribution_ZernikeMagnitude_Actin_4_4"
## [131] "RadialDistribution_ZernikeMagnitude_Actin_5_1"
## [132] "RadialDistribution_ZernikeMagnitude_Actin_5_3"
## [133] "RadialDistribution_ZernikeMagnitude_Actin_5_5"
## [134] "RadialDistribution_ZernikeMagnitude_Actin_6_0"
## [135] "RadialDistribution_ZernikeMagnitude_Actin_6_2"
## [136] "RadialDistribution_ZernikeMagnitude_Actin_6_4"
## [137] "RadialDistribution_ZernikeMagnitude_Actin_6_6"
## [138] "RadialDistribution_ZernikeMagnitude_Actin_7_1"
## [139] "RadialDistribution_ZernikeMagnitude_Actin_7_3"
## [140] "RadialDistribution_ZernikeMagnitude_Actin_7_5"
## [141] "RadialDistribution_ZernikeMagnitude_Actin_7_7"
## [142] "RadialDistribution_ZernikeMagnitude_Actin_8_0"
## [143] "RadialDistribution_ZernikeMagnitude_Actin_8_2"
## [144] "RadialDistribution_ZernikeMagnitude_Actin_8_4"
## [145] "RadialDistribution_ZernikeMagnitude_Actin_8_6"
## [146] "RadialDistribution_ZernikeMagnitude_Actin_8_8"
## [147] "RadialDistribution_ZernikeMagnitude_Actin_9_1"
## [148] "RadialDistribution_ZernikeMagnitude_Actin_9_3"
## [149] "RadialDistribution_ZernikeMagnitude_Actin_9_5"
## [150] "RadialDistribution_ZernikeMagnitude_Actin_9_7"
## [151] "RadialDistribution_ZernikeMagnitude_Actin_9_9"
## [152] "RadialDistribution_ZernikePhase_Actin_0_0"
## [153] "RadialDistribution_ZernikePhase_Actin_1_1"
## [154] "RadialDistribution_ZernikePhase_Actin_2_0"
## [155] "RadialDistribution_ZernikePhase_Actin_2_2"
## [156] "RadialDistribution_ZernikePhase_Actin_3_1"
## [157] "RadialDistribution_ZernikePhase_Actin_3_3"
## [158] "RadialDistribution_ZernikePhase_Actin_4_0"
## [159] "RadialDistribution_ZernikePhase_Actin_4_2"
## [160] "RadialDistribution_ZernikePhase_Actin_4_4"
## [161] "RadialDistribution_ZernikePhase_Actin_5_1"
## [162] "RadialDistribution_ZernikePhase_Actin_5_3"
## [163] "RadialDistribution_ZernikePhase_Actin_5_5"
## [164] "RadialDistribution_ZernikePhase_Actin_6_0"
## [165] "RadialDistribution_ZernikePhase_Actin_6_2"
## [166] "RadialDistribution_ZernikePhase_Actin_6_4"
## [167] "RadialDistribution_ZernikePhase_Actin_6_6"
## [168] "RadialDistribution_ZernikePhase_Actin_7_1"
## [169] "RadialDistribution_ZernikePhase_Actin_7_3"
## [170] "RadialDistribution_ZernikePhase_Actin_7_5"
## [171] "RadialDistribution_ZernikePhase_Actin_7_7"
## [172] "RadialDistribution_ZernikePhase_Actin_8_0"
## [173] "RadialDistribution_ZernikePhase_Actin_8_2"
## [174] "RadialDistribution_ZernikePhase_Actin_8_4"
## [175] "RadialDistribution_ZernikePhase_Actin_8_6"
## [176] "RadialDistribution_ZernikePhase_Actin_8_8"
## [177] "RadialDistribution_ZernikePhase_Actin_9_1"
## [178] "RadialDistribution_ZernikePhase_Actin_9_3"
## [179] "RadialDistribution_ZernikePhase_Actin_9_5"
## [180] "RadialDistribution_ZernikePhase_Actin_9_7"
## [181] "RadialDistribution_ZernikePhase_Actin_9_9"
## [182] "Texture_AngularSecondMoment_Actin_10_00_256"
## [183] "Texture_AngularSecondMoment_Actin_10_01_256"
## [184] "Texture_AngularSecondMoment_Actin_10_02_256"
## [185] "Texture_AngularSecondMoment_Actin_10_03_256"
## [186] "Texture_AngularSecondMoment_Actin_20_00_256"
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## [188] "Texture_AngularSecondMoment_Actin_20_02_256"
## [189] "Texture_AngularSecondMoment_Actin_20_03_256"
## [190] "Texture_AngularSecondMoment_Actin_5_00_256"
## [191] "Texture_AngularSecondMoment_Actin_5_01_256"
## [192] "Texture_AngularSecondMoment_Actin_5_02_256"
## [193] "Texture_AngularSecondMoment_Actin_5_03_256"
## [194] "Texture_Contrast_Actin_10_00_256"
## [195] "Texture_Contrast_Actin_10_01_256"
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## [202] "Texture_Contrast_Actin_5_00_256"
## [203] "Texture_Contrast_Actin_5_01_256"
## [204] "Texture_Contrast_Actin_5_02_256"
## [205] "Texture_Contrast_Actin_5_03_256"
## [206] "Texture_Correlation_Actin_10_00_256"
## [207] "Texture_Correlation_Actin_10_01_256"
## [208] "Texture_Correlation_Actin_10_02_256"
## [209] "Texture_Correlation_Actin_10_03_256"
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## [211] "Texture_Correlation_Actin_20_01_256"
## [212] "Texture_Correlation_Actin_20_02_256"
## [213] "Texture_Correlation_Actin_20_03_256"
## [214] "Texture_Correlation_Actin_5_00_256"
## [215] "Texture_Correlation_Actin_5_01_256"
## [216] "Texture_Correlation_Actin_5_02_256"
## [217] "Texture_Correlation_Actin_5_03_256"
## [218] "Texture_DifferenceEntropy_Actin_10_00_256"
## [219] "Texture_DifferenceEntropy_Actin_10_01_256"
## [220] "Texture_DifferenceEntropy_Actin_10_02_256"
## [221] "Texture_DifferenceEntropy_Actin_10_03_256"
## [222] "Texture_DifferenceEntropy_Actin_20_00_256"
## [223] "Texture_DifferenceEntropy_Actin_20_01_256"
## [224] "Texture_DifferenceEntropy_Actin_20_02_256"
## [225] "Texture_DifferenceEntropy_Actin_20_03_256"
## [226] "Texture_DifferenceEntropy_Actin_5_00_256"
## [227] "Texture_DifferenceEntropy_Actin_5_01_256"
## [228] "Texture_DifferenceEntropy_Actin_5_02_256"
## [229] "Texture_DifferenceEntropy_Actin_5_03_256"
## [230] "Texture_DifferenceVariance_Actin_10_00_256"
## [231] "Texture_DifferenceVariance_Actin_10_01_256"
## [232] "Texture_DifferenceVariance_Actin_10_02_256"
## [233] "Texture_DifferenceVariance_Actin_10_03_256"
## [234] "Texture_DifferenceVariance_Actin_20_00_256"
## [235] "Texture_DifferenceVariance_Actin_20_01_256"
## [236] "Texture_DifferenceVariance_Actin_20_02_256"
## [237] "Texture_DifferenceVariance_Actin_20_03_256"
## [238] "Texture_DifferenceVariance_Actin_5_00_256"
## [239] "Texture_DifferenceVariance_Actin_5_01_256"
## [240] "Texture_DifferenceVariance_Actin_5_02_256"
## [241] "Texture_DifferenceVariance_Actin_5_03_256"
## [242] "Texture_Entropy_Actin_10_00_256"
## [243] "Texture_Entropy_Actin_10_01_256"
## [244] "Texture_Entropy_Actin_10_02_256"
## [245] "Texture_Entropy_Actin_10_03_256"
## [246] "Texture_Entropy_Actin_20_00_256"
## [247] "Texture_Entropy_Actin_20_01_256"
## [248] "Texture_Entropy_Actin_20_02_256"
## [249] "Texture_Entropy_Actin_20_03_256"
## [250] "Texture_Entropy_Actin_5_00_256"
## [251] "Texture_Entropy_Actin_5_01_256"
## [252] "Texture_Entropy_Actin_5_02_256"
## [253] "Texture_Entropy_Actin_5_03_256"
## [254] "Texture_InfoMeas1_Actin_10_00_256"
## [255] "Texture_InfoMeas1_Actin_10_01_256"
## [256] "Texture_InfoMeas1_Actin_10_02_256"
## [257] "Texture_InfoMeas1_Actin_10_03_256"
## [258] "Texture_InfoMeas1_Actin_20_00_256"
## [259] "Texture_InfoMeas1_Actin_20_01_256"
## [260] "Texture_InfoMeas1_Actin_20_02_256"
## [261] "Texture_InfoMeas1_Actin_20_03_256"
## [262] "Texture_InfoMeas1_Actin_5_00_256"
## [263] "Texture_InfoMeas1_Actin_5_01_256"
## [264] "Texture_InfoMeas1_Actin_5_02_256"
## [265] "Texture_InfoMeas1_Actin_5_03_256"
## [266] "Texture_InfoMeas2_Actin_10_00_256"
## [267] "Texture_InfoMeas2_Actin_10_01_256"
## [268] "Texture_InfoMeas2_Actin_10_02_256"
## [269] "Texture_InfoMeas2_Actin_10_03_256"
## [270] "Texture_InfoMeas2_Actin_20_00_256"
## [271] "Texture_InfoMeas2_Actin_20_01_256"
## [272] "Texture_InfoMeas2_Actin_20_02_256"
## [273] "Texture_InfoMeas2_Actin_20_03_256"
## [274] "Texture_InfoMeas2_Actin_5_00_256"
## [275] "Texture_InfoMeas2_Actin_5_01_256"
## [276] "Texture_InfoMeas2_Actin_5_02_256"
## [277] "Texture_InfoMeas2_Actin_5_03_256"
## [278] "Texture_InverseDifferenceMoment_Actin_10_00_256"
## [279] "Texture_InverseDifferenceMoment_Actin_10_01_256"
## [280] "Texture_InverseDifferenceMoment_Actin_10_02_256"
## [281] "Texture_InverseDifferenceMoment_Actin_10_03_256"
## [282] "Texture_InverseDifferenceMoment_Actin_20_00_256"
## [283] "Texture_InverseDifferenceMoment_Actin_20_01_256"
## [284] "Texture_InverseDifferenceMoment_Actin_20_02_256"
## [285] "Texture_InverseDifferenceMoment_Actin_20_03_256"
## [286] "Texture_InverseDifferenceMoment_Actin_5_00_256"
## [287] "Texture_InverseDifferenceMoment_Actin_5_01_256"
## [288] "Texture_InverseDifferenceMoment_Actin_5_02_256"
## [289] "Texture_InverseDifferenceMoment_Actin_5_03_256"
## [290] "Texture_SumAverage_Actin_10_00_256"
## [291] "Texture_SumAverage_Actin_10_01_256"
## [292] "Texture_SumAverage_Actin_10_02_256"
## [293] "Texture_SumAverage_Actin_10_03_256"
## [294] "Texture_SumAverage_Actin_20_00_256"
## [295] "Texture_SumAverage_Actin_20_01_256"
## [296] "Texture_SumAverage_Actin_20_02_256"
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## [298] "Texture_SumAverage_Actin_5_00_256"
## [299] "Texture_SumAverage_Actin_5_01_256"
## [300] "Texture_SumAverage_Actin_5_02_256"
## [301] "Texture_SumAverage_Actin_5_03_256"
## [302] "Texture_SumEntropy_Actin_10_00_256"
## [303] "Texture_SumEntropy_Actin_10_01_256"
## [304] "Texture_SumEntropy_Actin_10_02_256"
## [305] "Texture_SumEntropy_Actin_10_03_256"
## [306] "Texture_SumEntropy_Actin_20_00_256"
## [307] "Texture_SumEntropy_Actin_20_01_256"
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## [313] "Texture_SumEntropy_Actin_5_03_256"
## [314] "Texture_SumVariance_Actin_10_00_256"
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## [337] "Texture_Variance_Actin_5_03_256"The selection helpers introduced here are a good start to select the variables of interest.
area_variables <-
getStatVariableNames(
object = object,
starts_with("AreaShape") & -contains(c("Zernike", "Center"))
)
area_variablesoutput
## [1] "AreaShape_Area" "AreaShape_BoundingBoxArea"
## [3] "AreaShape_BoundingBoxMaximum_X" "AreaShape_BoundingBoxMaximum_Y"
## [5] "AreaShape_BoundingBoxMinimum_X" "AreaShape_BoundingBoxMinimum_Y"
## [7] "AreaShape_Compactness" "AreaShape_Eccentricity"
## [9] "AreaShape_EquivalentDiameter" "AreaShape_EulerNumber"
## [11] "AreaShape_Extent" "AreaShape_FormFactor"
## [13] "AreaShape_MajorAxisLength" "AreaShape_MaxFeretDiameter"
## [15] "AreaShape_MaximumRadius" "AreaShape_MeanRadius"
## [17] "AreaShape_MedianRadius" "AreaShape_MinFeretDiameter"
## [19] "AreaShape_MinorAxisLength" "AreaShape_Orientation"
## [21] "AreaShape_Perimeter" "AreaShape_Solidity"Using the function addVariableSet() we can store these variables as a defined group in the cypro object and name that group. In this case we name the group of variables area as this is what they describe.
object <- addVariableSet(object, variable_names = area_variables, set_name = "area")
# obtain all stored variable set names with which to refer to them
getVariableSetNames(object)output
## [1] "intensity" "area"In case you need this defined set of variables as a character vector use getVariableSet().
getVariableSet(object, variable_set = "area")output
## [1] "AreaShape_Area" "AreaShape_BoundingBoxArea"
## [3] "AreaShape_BoundingBoxMaximum_X" "AreaShape_BoundingBoxMaximum_Y"
## [5] "AreaShape_BoundingBoxMinimum_X" "AreaShape_BoundingBoxMinimum_Y"
## [7] "AreaShape_Compactness" "AreaShape_Eccentricity"
## [9] "AreaShape_EquivalentDiameter" "AreaShape_EulerNumber"
## [11] "AreaShape_Extent" "AreaShape_FormFactor"
## [13] "AreaShape_MajorAxisLength" "AreaShape_MaxFeretDiameter"
## [15] "AreaShape_MaximumRadius" "AreaShape_MeanRadius"
## [17] "AreaShape_MedianRadius" "AreaShape_MinFeretDiameter"
## [19] "AreaShape_MinorAxisLength" "AreaShape_Orientation"
## [21] "AreaShape_Perimeter" "AreaShape_Solidity"How useful these variable sets are is exemplified in particular in the tutorials on dimensional reduction, clustering and correlation.