Make sure to be familiar with the following tutorials before proceeding:
There are several situations in which renaming of variables or groups is desirable. cypro provides functions to do that conveniently even in the light of the multitude of variables researchers are confronted during quantification of automated imaging experiments. As this includes implementation of the well thoght out renaming system of the tidyverse knowledge around the packages stringr, stringi and dplyr is helpful (though not necessary). Renaming content is possible via two types of functions:
Simple rename*()-functions rename individual content one by one with the syntax new_name = old_name. It implements the concept of dplyr::rename()
rename*With()- functions implement dplyr::rename_with() that allows to rename variables with functions. They require knowledge about the stringr package but are quite powerful with a bit of practice.
The cell data.frames obtained via getStatsDf() and via getTracksDf()contain the data variables according to which analysis is conducted.
vars <- getTrackVariableNames(object)
print(vars[1:5])output
## [1] "AreaShape_Area" "AreaShape_BoundingBoxArea"
## [3] "AreaShape_BoundingBoxMaximum_X" "AreaShape_BoundingBoxMaximum_Y"
## [5] "AreaShape_BoundingBoxMinimum_X"For instance, renaming area related variables might be useful as the redundant prefix forces a lot of unnecessary typing. However, this approach can get quite cumbersome in case of more than 300 variables whose names, too, could be adjusted to more concise versions for more convenient analysis with less typing.
object <- renameTracksDf(object, Area = AreaShape_Area)
# notice the renamed first variable
getTrackVariableNames(object)output
## [1] "Area"
## [2] "AreaShape_BoundingBoxArea"
## [3] "AreaShape_BoundingBoxMaximum_X"
## [4] "AreaShape_BoundingBoxMaximum_Y"
## [5] "AreaShape_BoundingBoxMinimum_X"
## [6] "AreaShape_BoundingBoxMinimum_Y"
## [7] "AreaShape_Center_X"
## [8] "AreaShape_Center_Y"
## [9] "AreaShape_Compactness"
## [10] "AreaShape_Eccentricity"
## [11] "AreaShape_EquivalentDiameter"
## [12] "AreaShape_EulerNumber"
## [13] "AreaShape_Extent"
## [14] "AreaShape_FormFactor"
## [15] "AreaShape_MajorAxisLength"
## [16] "AreaShape_MaxFeretDiameter"
## [17] "AreaShape_MaximumRadius"
## [18] "AreaShape_MeanRadius"
## [19] "AreaShape_MedianRadius"
## [20] "AreaShape_MinFeretDiameter"
## [21] "AreaShape_MinorAxisLength"
## [22] "AreaShape_Orientation"
## [23] "AreaShape_Perimeter"
## [24] "AreaShape_Solidity"
## [25] "AreaShape_Zernike_0_0"
## [26] "AreaShape_Zernike_1_1"
## [27] "AreaShape_Zernike_2_0"
## [28] "AreaShape_Zernike_2_2"
## [29] "AreaShape_Zernike_3_1"
## [30] "AreaShape_Zernike_3_3"
## [31] "AreaShape_Zernike_4_0"
## [32] "AreaShape_Zernike_4_2"
## [33] "AreaShape_Zernike_4_4"
## [34] "AreaShape_Zernike_5_1"
## [35] "AreaShape_Zernike_5_3"
## [36] "AreaShape_Zernike_5_5"
## [37] "AreaShape_Zernike_6_0"
## [38] "AreaShape_Zernike_6_2"
## [39] "AreaShape_Zernike_6_4"
## [40] "AreaShape_Zernike_6_6"
## [41] "AreaShape_Zernike_7_1"
## [42] "AreaShape_Zernike_7_3"
## [43] "AreaShape_Zernike_7_5"
## [44] "AreaShape_Zernike_7_7"
## [45] "AreaShape_Zernike_8_0"
## [46] "AreaShape_Zernike_8_2"
## [47] "AreaShape_Zernike_8_4"
## [48] "AreaShape_Zernike_8_6"
## [49] "AreaShape_Zernike_8_8"
## [50] "AreaShape_Zernike_9_1"
## [51] "AreaShape_Zernike_9_3"
## [52] "AreaShape_Zernike_9_5"
## [53] "AreaShape_Zernike_9_7"
## [54] "AreaShape_Zernike_9_9"
## [55] "Children_Cytoplasm_Count"
## [56] "Granularity_10_Actin"
## [57] "Granularity_11_Actin"
## [58] "Granularity_12_Actin"
## [59] "Granularity_13_Actin"
## [60] "Granularity_14_Actin"
## [61] "Granularity_15_Actin"
## [62] "Granularity_16_Actin"
## [63] "Granularity_1_Actin"
## [64] "Granularity_2_Actin"
## [65] "Granularity_3_Actin"
## [66] "Granularity_4_Actin"
## [67] "Granularity_5_Actin"
## [68] "Granularity_6_Actin"
## [69] "Granularity_7_Actin"
## [70] "Granularity_8_Actin"
## [71] "Granularity_9_Actin"
## [72] "Intensity_IntegratedIntensityEdge_Actin"
## [73] "Intensity_IntegratedIntensity_Actin"
## [74] "Intensity_LowerQuartileIntensity_Actin"
## [75] "Intensity_MADIntensity_Actin"
## [76] "Intensity_MassDisplacement_Actin"
## [77] "Intensity_MaxIntensityEdge_Actin"
## [78] "Intensity_MaxIntensity_Actin"
## [79] "Intensity_MeanIntensityEdge_Actin"
## [80] "Intensity_MeanIntensity_Actin"
## [81] "Intensity_MedianIntensity_Actin"
## [82] "Intensity_MinIntensityEdge_Actin"
## [83] "Intensity_MinIntensity_Actin"
## [84] "Intensity_StdIntensityEdge_Actin"
## [85] "Intensity_StdIntensity_Actin"
## [86] "Intensity_UpperQuartileIntensity_Actin"
## [87] "Location_CenterMassIntensity_X_Actin"
## [88] "Location_CenterMassIntensity_Y_Actin"
## [89] "Location_MaxIntensity_X_Actin"
## [90] "Location_MaxIntensity_Y_Actin"
## [91] "Neighbors_AngleBetweenNeighbors_10"
## [92] "Neighbors_AngleBetweenNeighbors_Adjacent"
## [93] "Neighbors_FirstClosestDistance_10"
## [94] "Neighbors_FirstClosestDistance_Adjacent"
## [95] "Neighbors_FirstClosestObjectNumber_10"
## [96] "Neighbors_FirstClosestObjectNumber_Adjacent"
## [97] "Neighbors_NumberOfNeighbors_10"
## [98] "Neighbors_NumberOfNeighbors_Adjacent"
## [99] "Neighbors_PercentTouching_10"
## [100] "Neighbors_PercentTouching_Adjacent"
## [101] "Neighbors_SecondClosestDistance_10"
## [102] "Neighbors_SecondClosestDistance_Adjacent"
## [103] "Neighbors_SecondClosestObjectNumber_10"
## [104] "Neighbors_SecondClosestObjectNumber_Adjacent"
## [105] "Number_Object_Number"
## [106] "Parent_Nuclei"
## [107] "RadialDistribution_FracAtD_Actin_1of4"
## [108] "RadialDistribution_FracAtD_Actin_2of4"
## [109] "RadialDistribution_FracAtD_Actin_3of4"
## [110] "RadialDistribution_FracAtD_Actin_4of4"
## [111] "RadialDistribution_MeanFrac_Actin_1of4"
## [112] "RadialDistribution_MeanFrac_Actin_2of4"
## [113] "RadialDistribution_MeanFrac_Actin_3of4"
## [114] "RadialDistribution_MeanFrac_Actin_4of4"
## [115] "RadialDistribution_RadialCV_Actin_1of4"
## [116] "RadialDistribution_RadialCV_Actin_2of4"
## [117] "RadialDistribution_RadialCV_Actin_3of4"
## [118] "RadialDistribution_RadialCV_Actin_4of4"
## [119] "RadialDistribution_ZernikeMagnitude_Actin_0_0"
## [120] "RadialDistribution_ZernikeMagnitude_Actin_1_1"
## [121] "RadialDistribution_ZernikeMagnitude_Actin_2_0"
## [122] "RadialDistribution_ZernikeMagnitude_Actin_2_2"
## [123] "RadialDistribution_ZernikeMagnitude_Actin_3_1"
## [124] "RadialDistribution_ZernikeMagnitude_Actin_3_3"
## [125] "RadialDistribution_ZernikeMagnitude_Actin_4_0"
## [126] "RadialDistribution_ZernikeMagnitude_Actin_4_2"
## [127] "RadialDistribution_ZernikeMagnitude_Actin_4_4"
## [128] "RadialDistribution_ZernikeMagnitude_Actin_5_1"
## [129] "RadialDistribution_ZernikeMagnitude_Actin_5_3"
## [130] "RadialDistribution_ZernikeMagnitude_Actin_5_5"
## [131] "RadialDistribution_ZernikeMagnitude_Actin_6_0"
## [132] "RadialDistribution_ZernikeMagnitude_Actin_6_2"
## [133] "RadialDistribution_ZernikeMagnitude_Actin_6_4"
## [134] "RadialDistribution_ZernikeMagnitude_Actin_6_6"
## [135] "RadialDistribution_ZernikeMagnitude_Actin_7_1"
## [136] "RadialDistribution_ZernikeMagnitude_Actin_7_3"
## [137] "RadialDistribution_ZernikeMagnitude_Actin_7_5"
## [138] "RadialDistribution_ZernikeMagnitude_Actin_7_7"
## [139] "RadialDistribution_ZernikeMagnitude_Actin_8_0"
## [140] "RadialDistribution_ZernikeMagnitude_Actin_8_2"
## [141] "RadialDistribution_ZernikeMagnitude_Actin_8_4"
## [142] "RadialDistribution_ZernikeMagnitude_Actin_8_6"
## [143] "RadialDistribution_ZernikeMagnitude_Actin_8_8"
## [144] "RadialDistribution_ZernikeMagnitude_Actin_9_1"
## [145] "RadialDistribution_ZernikeMagnitude_Actin_9_3"
## [146] "RadialDistribution_ZernikeMagnitude_Actin_9_5"
## [147] "RadialDistribution_ZernikeMagnitude_Actin_9_7"
## [148] "RadialDistribution_ZernikeMagnitude_Actin_9_9"
## [149] "RadialDistribution_ZernikePhase_Actin_0_0"
## [150] "RadialDistribution_ZernikePhase_Actin_1_1"
## [151] "RadialDistribution_ZernikePhase_Actin_2_0"
## [152] "RadialDistribution_ZernikePhase_Actin_2_2"
## [153] "RadialDistribution_ZernikePhase_Actin_3_1"
## [154] "RadialDistribution_ZernikePhase_Actin_3_3"
## [155] "RadialDistribution_ZernikePhase_Actin_4_0"
## [156] "RadialDistribution_ZernikePhase_Actin_4_2"
## [157] "RadialDistribution_ZernikePhase_Actin_4_4"
## [158] "RadialDistribution_ZernikePhase_Actin_5_1"
## [159] "RadialDistribution_ZernikePhase_Actin_5_3"
## [160] "RadialDistribution_ZernikePhase_Actin_5_5"
## [161] "RadialDistribution_ZernikePhase_Actin_6_0"
## [162] "RadialDistribution_ZernikePhase_Actin_6_2"
## [163] "RadialDistribution_ZernikePhase_Actin_6_4"
## [164] "RadialDistribution_ZernikePhase_Actin_6_6"
## [165] "RadialDistribution_ZernikePhase_Actin_7_1"
## [166] "RadialDistribution_ZernikePhase_Actin_7_3"
## [167] "RadialDistribution_ZernikePhase_Actin_7_5"
## [168] "RadialDistribution_ZernikePhase_Actin_7_7"
## [169] "RadialDistribution_ZernikePhase_Actin_8_0"
## [170] "RadialDistribution_ZernikePhase_Actin_8_2"
## [171] "RadialDistribution_ZernikePhase_Actin_8_4"
## [172] "RadialDistribution_ZernikePhase_Actin_8_6"
## [173] "RadialDistribution_ZernikePhase_Actin_8_8"
## [174] "RadialDistribution_ZernikePhase_Actin_9_1"
## [175] "RadialDistribution_ZernikePhase_Actin_9_3"
## [176] "RadialDistribution_ZernikePhase_Actin_9_5"
## [177] "RadialDistribution_ZernikePhase_Actin_9_7"
## [178] "RadialDistribution_ZernikePhase_Actin_9_9"
## [179] "Texture_AngularSecondMoment_Actin_10_00_256"
## [180] "Texture_AngularSecondMoment_Actin_10_01_256"
## [181] "Texture_AngularSecondMoment_Actin_10_02_256"
## [182] "Texture_AngularSecondMoment_Actin_10_03_256"
## [183] "Texture_AngularSecondMoment_Actin_20_00_256"
## [184] "Texture_AngularSecondMoment_Actin_20_01_256"
## [185] "Texture_AngularSecondMoment_Actin_20_02_256"
## [186] "Texture_AngularSecondMoment_Actin_20_03_256"
## [187] "Texture_AngularSecondMoment_Actin_5_00_256"
## [188] "Texture_AngularSecondMoment_Actin_5_01_256"
## [189] "Texture_AngularSecondMoment_Actin_5_02_256"
## [190] "Texture_AngularSecondMoment_Actin_5_03_256"
## [191] "Texture_Contrast_Actin_10_00_256"
## [192] "Texture_Contrast_Actin_10_01_256"
## [193] "Texture_Contrast_Actin_10_02_256"
## [194] "Texture_Contrast_Actin_10_03_256"
## [195] "Texture_Contrast_Actin_20_00_256"
## [196] "Texture_Contrast_Actin_20_01_256"
## [197] "Texture_Contrast_Actin_20_02_256"
## [198] "Texture_Contrast_Actin_20_03_256"
## [199] "Texture_Contrast_Actin_5_00_256"
## [200] "Texture_Contrast_Actin_5_01_256"
## [201] "Texture_Contrast_Actin_5_02_256"
## [202] "Texture_Contrast_Actin_5_03_256"
## [203] "Texture_Correlation_Actin_10_00_256"
## [204] "Texture_Correlation_Actin_10_01_256"
## [205] "Texture_Correlation_Actin_10_02_256"
## [206] "Texture_Correlation_Actin_10_03_256"
## [207] "Texture_Correlation_Actin_20_00_256"
## [208] "Texture_Correlation_Actin_20_01_256"
## [209] "Texture_Correlation_Actin_20_02_256"
## [210] "Texture_Correlation_Actin_20_03_256"
## [211] "Texture_Correlation_Actin_5_00_256"
## [212] "Texture_Correlation_Actin_5_01_256"
## [213] "Texture_Correlation_Actin_5_02_256"
## [214] "Texture_Correlation_Actin_5_03_256"
## [215] "Texture_DifferenceEntropy_Actin_10_00_256"
## [216] "Texture_DifferenceEntropy_Actin_10_01_256"
## [217] "Texture_DifferenceEntropy_Actin_10_02_256"
## [218] "Texture_DifferenceEntropy_Actin_10_03_256"
## [219] "Texture_DifferenceEntropy_Actin_20_00_256"
## [220] "Texture_DifferenceEntropy_Actin_20_01_256"
## [221] "Texture_DifferenceEntropy_Actin_20_02_256"
## [222] "Texture_DifferenceEntropy_Actin_20_03_256"
## [223] "Texture_DifferenceEntropy_Actin_5_00_256"
## [224] "Texture_DifferenceEntropy_Actin_5_01_256"
## [225] "Texture_DifferenceEntropy_Actin_5_02_256"
## [226] "Texture_DifferenceEntropy_Actin_5_03_256"
## [227] "Texture_DifferenceVariance_Actin_10_00_256"
## [228] "Texture_DifferenceVariance_Actin_10_01_256"
## [229] "Texture_DifferenceVariance_Actin_10_02_256"
## [230] "Texture_DifferenceVariance_Actin_10_03_256"
## [231] "Texture_DifferenceVariance_Actin_20_00_256"
## [232] "Texture_DifferenceVariance_Actin_20_01_256"
## [233] "Texture_DifferenceVariance_Actin_20_02_256"
## [234] "Texture_DifferenceVariance_Actin_20_03_256"
## [235] "Texture_DifferenceVariance_Actin_5_00_256"
## [236] "Texture_DifferenceVariance_Actin_5_01_256"
## [237] "Texture_DifferenceVariance_Actin_5_02_256"
## [238] "Texture_DifferenceVariance_Actin_5_03_256"
## [239] "Texture_Entropy_Actin_10_00_256"
## [240] "Texture_Entropy_Actin_10_01_256"
## [241] "Texture_Entropy_Actin_10_02_256"
## [242] "Texture_Entropy_Actin_10_03_256"
## [243] "Texture_Entropy_Actin_20_00_256"
## [244] "Texture_Entropy_Actin_20_01_256"
## [245] "Texture_Entropy_Actin_20_02_256"
## [246] "Texture_Entropy_Actin_20_03_256"
## [247] "Texture_Entropy_Actin_5_00_256"
## [248] "Texture_Entropy_Actin_5_01_256"
## [249] "Texture_Entropy_Actin_5_02_256"
## [250] "Texture_Entropy_Actin_5_03_256"
## [251] "Texture_InfoMeas1_Actin_10_00_256"
## [252] "Texture_InfoMeas1_Actin_10_01_256"
## [253] "Texture_InfoMeas1_Actin_10_02_256"
## [254] "Texture_InfoMeas1_Actin_10_03_256"
## [255] "Texture_InfoMeas1_Actin_20_00_256"
## [256] "Texture_InfoMeas1_Actin_20_01_256"
## [257] "Texture_InfoMeas1_Actin_20_02_256"
## [258] "Texture_InfoMeas1_Actin_20_03_256"
## [259] "Texture_InfoMeas1_Actin_5_00_256"
## [260] "Texture_InfoMeas1_Actin_5_01_256"
## [261] "Texture_InfoMeas1_Actin_5_02_256"
## [262] "Texture_InfoMeas1_Actin_5_03_256"
## [263] "Texture_InfoMeas2_Actin_10_00_256"
## [264] "Texture_InfoMeas2_Actin_10_01_256"
## [265] "Texture_InfoMeas2_Actin_10_02_256"
## [266] "Texture_InfoMeas2_Actin_10_03_256"
## [267] "Texture_InfoMeas2_Actin_20_00_256"
## [268] "Texture_InfoMeas2_Actin_20_01_256"
## [269] "Texture_InfoMeas2_Actin_20_02_256"
## [270] "Texture_InfoMeas2_Actin_20_03_256"
## [271] "Texture_InfoMeas2_Actin_5_00_256"
## [272] "Texture_InfoMeas2_Actin_5_01_256"
## [273] "Texture_InfoMeas2_Actin_5_02_256"
## [274] "Texture_InfoMeas2_Actin_5_03_256"
## [275] "Texture_InverseDifferenceMoment_Actin_10_00_256"
## [276] "Texture_InverseDifferenceMoment_Actin_10_01_256"
## [277] "Texture_InverseDifferenceMoment_Actin_10_02_256"
## [278] "Texture_InverseDifferenceMoment_Actin_10_03_256"
## [279] "Texture_InverseDifferenceMoment_Actin_20_00_256"
## [280] "Texture_InverseDifferenceMoment_Actin_20_01_256"
## [281] "Texture_InverseDifferenceMoment_Actin_20_02_256"
## [282] "Texture_InverseDifferenceMoment_Actin_20_03_256"
## [283] "Texture_InverseDifferenceMoment_Actin_5_00_256"
## [284] "Texture_InverseDifferenceMoment_Actin_5_01_256"
## [285] "Texture_InverseDifferenceMoment_Actin_5_02_256"
## [286] "Texture_InverseDifferenceMoment_Actin_5_03_256"
## [287] "Texture_SumAverage_Actin_10_00_256"
## [288] "Texture_SumAverage_Actin_10_01_256"
## [289] "Texture_SumAverage_Actin_10_02_256"
## [290] "Texture_SumAverage_Actin_10_03_256"
## [291] "Texture_SumAverage_Actin_20_00_256"
## [292] "Texture_SumAverage_Actin_20_01_256"
## [293] "Texture_SumAverage_Actin_20_02_256"
## [294] "Texture_SumAverage_Actin_20_03_256"
## [295] "Texture_SumAverage_Actin_5_00_256"
## [296] "Texture_SumAverage_Actin_5_01_256"
## [297] "Texture_SumAverage_Actin_5_02_256"
## [298] "Texture_SumAverage_Actin_5_03_256"
## [299] "Texture_SumEntropy_Actin_10_00_256"
## [300] "Texture_SumEntropy_Actin_10_01_256"
## [301] "Texture_SumEntropy_Actin_10_02_256"
## [302] "Texture_SumEntropy_Actin_10_03_256"
## [303] "Texture_SumEntropy_Actin_20_00_256"
## [304] "Texture_SumEntropy_Actin_20_01_256"
## [305] "Texture_SumEntropy_Actin_20_02_256"
## [306] "Texture_SumEntropy_Actin_20_03_256"
## [307] "Texture_SumEntropy_Actin_5_00_256"
## [308] "Texture_SumEntropy_Actin_5_01_256"
## [309] "Texture_SumEntropy_Actin_5_02_256"
## [310] "Texture_SumEntropy_Actin_5_03_256"
## [311] "Texture_SumVariance_Actin_10_00_256"
## [312] "Texture_SumVariance_Actin_10_01_256"
## [313] "Texture_SumVariance_Actin_10_02_256"
## [314] "Texture_SumVariance_Actin_10_03_256"
## [315] "Texture_SumVariance_Actin_20_00_256"
## [316] "Texture_SumVariance_Actin_20_01_256"
## [317] "Texture_SumVariance_Actin_20_02_256"
## [318] "Texture_SumVariance_Actin_20_03_256"
## [319] "Texture_SumVariance_Actin_5_00_256"
## [320] "Texture_SumVariance_Actin_5_01_256"
## [321] "Texture_SumVariance_Actin_5_02_256"
## [322] "Texture_SumVariance_Actin_5_03_256"
## [323] "Texture_Variance_Actin_10_00_256"
## [324] "Texture_Variance_Actin_10_01_256"
## [325] "Texture_Variance_Actin_10_02_256"
## [326] "Texture_Variance_Actin_10_03_256"
## [327] "Texture_Variance_Actin_20_00_256"
## [328] "Texture_Variance_Actin_20_01_256"
## [329] "Texture_Variance_Actin_20_02_256"
## [330] "Texture_Variance_Actin_20_03_256"
## [331] "Texture_Variance_Actin_5_00_256"
## [332] "Texture_Variance_Actin_5_01_256"
## [333] "Texture_Variance_Actin_5_02_256"
## [334] "Texture_Variance_Actin_5_03_256"This is where renameStatsDfWith() comes in handy. Two examples:
# replace the AreaShape prefix with a shorter version
object <-
renameTracksDfWith(
object = object,
.fn = ~ str_replace_all(.x, pattern = "AreaShape_", replacement = "AS_")
)
getTrackVariableNames(object)output
## [1] "Area"
## [2] "AS_BoundingBoxArea"
## [3] "AS_BoundingBoxMaximum_X"
## [4] "AS_BoundingBoxMaximum_Y"
## [5] "AS_BoundingBoxMinimum_X"
## [6] "AS_BoundingBoxMinimum_Y"
## [7] "AS_Center_X"
## [8] "AS_Center_Y"
## [9] "AS_Compactness"
## [10] "AS_Eccentricity"
## [11] "AS_EquivalentDiameter"
## [12] "AS_EulerNumber"
## [13] "AS_Extent"
## [14] "AS_FormFactor"
## [15] "AS_MajorAxisLength"
## [16] "AS_MaxFeretDiameter"
## [17] "AS_MaximumRadius"
## [18] "AS_MeanRadius"
## [19] "AS_MedianRadius"
## [20] "AS_MinFeretDiameter"
## [21] "AS_MinorAxisLength"
## [22] "AS_Orientation"
## [23] "AS_Perimeter"
## [24] "AS_Solidity"
## [25] "AS_Zernike_0_0"
## [26] "AS_Zernike_1_1"
## [27] "AS_Zernike_2_0"
## [28] "AS_Zernike_2_2"
## [29] "AS_Zernike_3_1"
## [30] "AS_Zernike_3_3"
## [31] "AS_Zernike_4_0"
## [32] "AS_Zernike_4_2"
## [33] "AS_Zernike_4_4"
## [34] "AS_Zernike_5_1"
## [35] "AS_Zernike_5_3"
## [36] "AS_Zernike_5_5"
## [37] "AS_Zernike_6_0"
## [38] "AS_Zernike_6_2"
## [39] "AS_Zernike_6_4"
## [40] "AS_Zernike_6_6"
## [41] "AS_Zernike_7_1"
## [42] "AS_Zernike_7_3"
## [43] "AS_Zernike_7_5"
## [44] "AS_Zernike_7_7"
## [45] "AS_Zernike_8_0"
## [46] "AS_Zernike_8_2"
## [47] "AS_Zernike_8_4"
## [48] "AS_Zernike_8_6"
## [49] "AS_Zernike_8_8"
## [50] "AS_Zernike_9_1"
## [51] "AS_Zernike_9_3"
## [52] "AS_Zernike_9_5"
## [53] "AS_Zernike_9_7"
## [54] "AS_Zernike_9_9"
## [55] "Children_Cytoplasm_Count"
## [56] "Granularity_10_Actin"
## [57] "Granularity_11_Actin"
## [58] "Granularity_12_Actin"
## [59] "Granularity_13_Actin"
## [60] "Granularity_14_Actin"
## [61] "Granularity_15_Actin"
## [62] "Granularity_16_Actin"
## [63] "Granularity_1_Actin"
## [64] "Granularity_2_Actin"
## [65] "Granularity_3_Actin"
## [66] "Granularity_4_Actin"
## [67] "Granularity_5_Actin"
## [68] "Granularity_6_Actin"
## [69] "Granularity_7_Actin"
## [70] "Granularity_8_Actin"
## [71] "Granularity_9_Actin"
## [72] "Intensity_IntegratedIntensityEdge_Actin"
## [73] "Intensity_IntegratedIntensity_Actin"
## [74] "Intensity_LowerQuartileIntensity_Actin"
## [75] "Intensity_MADIntensity_Actin"
## [76] "Intensity_MassDisplacement_Actin"
## [77] "Intensity_MaxIntensityEdge_Actin"
## [78] "Intensity_MaxIntensity_Actin"
## [79] "Intensity_MeanIntensityEdge_Actin"
## [80] "Intensity_MeanIntensity_Actin"
## [81] "Intensity_MedianIntensity_Actin"
## [82] "Intensity_MinIntensityEdge_Actin"
## [83] "Intensity_MinIntensity_Actin"
## [84] "Intensity_StdIntensityEdge_Actin"
## [85] "Intensity_StdIntensity_Actin"
## [86] "Intensity_UpperQuartileIntensity_Actin"
## [87] "Location_CenterMassIntensity_X_Actin"
## [88] "Location_CenterMassIntensity_Y_Actin"
## [89] "Location_MaxIntensity_X_Actin"
## [90] "Location_MaxIntensity_Y_Actin"
## [91] "Neighbors_AngleBetweenNeighbors_10"
## [92] "Neighbors_AngleBetweenNeighbors_Adjacent"
## [93] "Neighbors_FirstClosestDistance_10"
## [94] "Neighbors_FirstClosestDistance_Adjacent"
## [95] "Neighbors_FirstClosestObjectNumber_10"
## [96] "Neighbors_FirstClosestObjectNumber_Adjacent"
## [97] "Neighbors_NumberOfNeighbors_10"
## [98] "Neighbors_NumberOfNeighbors_Adjacent"
## [99] "Neighbors_PercentTouching_10"
## [100] "Neighbors_PercentTouching_Adjacent"
## [101] "Neighbors_SecondClosestDistance_10"
## [102] "Neighbors_SecondClosestDistance_Adjacent"
## [103] "Neighbors_SecondClosestObjectNumber_10"
## [104] "Neighbors_SecondClosestObjectNumber_Adjacent"
## [105] "Number_Object_Number"
## [106] "Parent_Nuclei"
## [107] "RadialDistribution_FracAtD_Actin_1of4"
## [108] "RadialDistribution_FracAtD_Actin_2of4"
## [109] "RadialDistribution_FracAtD_Actin_3of4"
## [110] "RadialDistribution_FracAtD_Actin_4of4"
## [111] "RadialDistribution_MeanFrac_Actin_1of4"
## [112] "RadialDistribution_MeanFrac_Actin_2of4"
## [113] "RadialDistribution_MeanFrac_Actin_3of4"
## [114] "RadialDistribution_MeanFrac_Actin_4of4"
## [115] "RadialDistribution_RadialCV_Actin_1of4"
## [116] "RadialDistribution_RadialCV_Actin_2of4"
## [117] "RadialDistribution_RadialCV_Actin_3of4"
## [118] "RadialDistribution_RadialCV_Actin_4of4"
## [119] "RadialDistribution_ZernikeMagnitude_Actin_0_0"
## [120] "RadialDistribution_ZernikeMagnitude_Actin_1_1"
## [121] "RadialDistribution_ZernikeMagnitude_Actin_2_0"
## [122] "RadialDistribution_ZernikeMagnitude_Actin_2_2"
## [123] "RadialDistribution_ZernikeMagnitude_Actin_3_1"
## [124] "RadialDistribution_ZernikeMagnitude_Actin_3_3"
## [125] "RadialDistribution_ZernikeMagnitude_Actin_4_0"
## [126] "RadialDistribution_ZernikeMagnitude_Actin_4_2"
## [127] "RadialDistribution_ZernikeMagnitude_Actin_4_4"
## [128] "RadialDistribution_ZernikeMagnitude_Actin_5_1"
## [129] "RadialDistribution_ZernikeMagnitude_Actin_5_3"
## [130] "RadialDistribution_ZernikeMagnitude_Actin_5_5"
## [131] "RadialDistribution_ZernikeMagnitude_Actin_6_0"
## [132] "RadialDistribution_ZernikeMagnitude_Actin_6_2"
## [133] "RadialDistribution_ZernikeMagnitude_Actin_6_4"
## [134] "RadialDistribution_ZernikeMagnitude_Actin_6_6"
## [135] "RadialDistribution_ZernikeMagnitude_Actin_7_1"
## [136] "RadialDistribution_ZernikeMagnitude_Actin_7_3"
## [137] "RadialDistribution_ZernikeMagnitude_Actin_7_5"
## [138] "RadialDistribution_ZernikeMagnitude_Actin_7_7"
## [139] "RadialDistribution_ZernikeMagnitude_Actin_8_0"
## [140] "RadialDistribution_ZernikeMagnitude_Actin_8_2"
## [141] "RadialDistribution_ZernikeMagnitude_Actin_8_4"
## [142] "RadialDistribution_ZernikeMagnitude_Actin_8_6"
## [143] "RadialDistribution_ZernikeMagnitude_Actin_8_8"
## [144] "RadialDistribution_ZernikeMagnitude_Actin_9_1"
## [145] "RadialDistribution_ZernikeMagnitude_Actin_9_3"
## [146] "RadialDistribution_ZernikeMagnitude_Actin_9_5"
## [147] "RadialDistribution_ZernikeMagnitude_Actin_9_7"
## [148] "RadialDistribution_ZernikeMagnitude_Actin_9_9"
## [149] "RadialDistribution_ZernikePhase_Actin_0_0"
## [150] "RadialDistribution_ZernikePhase_Actin_1_1"
## [151] "RadialDistribution_ZernikePhase_Actin_2_0"
## [152] "RadialDistribution_ZernikePhase_Actin_2_2"
## [153] "RadialDistribution_ZernikePhase_Actin_3_1"
## [154] "RadialDistribution_ZernikePhase_Actin_3_3"
## [155] "RadialDistribution_ZernikePhase_Actin_4_0"
## [156] "RadialDistribution_ZernikePhase_Actin_4_2"
## [157] "RadialDistribution_ZernikePhase_Actin_4_4"
## [158] "RadialDistribution_ZernikePhase_Actin_5_1"
## [159] "RadialDistribution_ZernikePhase_Actin_5_3"
## [160] "RadialDistribution_ZernikePhase_Actin_5_5"
## [161] "RadialDistribution_ZernikePhase_Actin_6_0"
## [162] "RadialDistribution_ZernikePhase_Actin_6_2"
## [163] "RadialDistribution_ZernikePhase_Actin_6_4"
## [164] "RadialDistribution_ZernikePhase_Actin_6_6"
## [165] "RadialDistribution_ZernikePhase_Actin_7_1"
## [166] "RadialDistribution_ZernikePhase_Actin_7_3"
## [167] "RadialDistribution_ZernikePhase_Actin_7_5"
## [168] "RadialDistribution_ZernikePhase_Actin_7_7"
## [169] "RadialDistribution_ZernikePhase_Actin_8_0"
## [170] "RadialDistribution_ZernikePhase_Actin_8_2"
## [171] "RadialDistribution_ZernikePhase_Actin_8_4"
## [172] "RadialDistribution_ZernikePhase_Actin_8_6"
## [173] "RadialDistribution_ZernikePhase_Actin_8_8"
## [174] "RadialDistribution_ZernikePhase_Actin_9_1"
## [175] "RadialDistribution_ZernikePhase_Actin_9_3"
## [176] "RadialDistribution_ZernikePhase_Actin_9_5"
## [177] "RadialDistribution_ZernikePhase_Actin_9_7"
## [178] "RadialDistribution_ZernikePhase_Actin_9_9"
## [179] "Texture_AngularSecondMoment_Actin_10_00_256"
## [180] "Texture_AngularSecondMoment_Actin_10_01_256"
## [181] "Texture_AngularSecondMoment_Actin_10_02_256"
## [182] "Texture_AngularSecondMoment_Actin_10_03_256"
## [183] "Texture_AngularSecondMoment_Actin_20_00_256"
## [184] "Texture_AngularSecondMoment_Actin_20_01_256"
## [185] "Texture_AngularSecondMoment_Actin_20_02_256"
## [186] "Texture_AngularSecondMoment_Actin_20_03_256"
## [187] "Texture_AngularSecondMoment_Actin_5_00_256"
## [188] "Texture_AngularSecondMoment_Actin_5_01_256"
## [189] "Texture_AngularSecondMoment_Actin_5_02_256"
## [190] "Texture_AngularSecondMoment_Actin_5_03_256"
## [191] "Texture_Contrast_Actin_10_00_256"
## [192] "Texture_Contrast_Actin_10_01_256"
## [193] "Texture_Contrast_Actin_10_02_256"
## [194] "Texture_Contrast_Actin_10_03_256"
## [195] "Texture_Contrast_Actin_20_00_256"
## [196] "Texture_Contrast_Actin_20_01_256"
## [197] "Texture_Contrast_Actin_20_02_256"
## [198] "Texture_Contrast_Actin_20_03_256"
## [199] "Texture_Contrast_Actin_5_00_256"
## [200] "Texture_Contrast_Actin_5_01_256"
## [201] "Texture_Contrast_Actin_5_02_256"
## [202] "Texture_Contrast_Actin_5_03_256"
## [203] "Texture_Correlation_Actin_10_00_256"
## [204] "Texture_Correlation_Actin_10_01_256"
## [205] "Texture_Correlation_Actin_10_02_256"
## [206] "Texture_Correlation_Actin_10_03_256"
## [207] "Texture_Correlation_Actin_20_00_256"
## [208] "Texture_Correlation_Actin_20_01_256"
## [209] "Texture_Correlation_Actin_20_02_256"
## [210] "Texture_Correlation_Actin_20_03_256"
## [211] "Texture_Correlation_Actin_5_00_256"
## [212] "Texture_Correlation_Actin_5_01_256"
## [213] "Texture_Correlation_Actin_5_02_256"
## [214] "Texture_Correlation_Actin_5_03_256"
## [215] "Texture_DifferenceEntropy_Actin_10_00_256"
## [216] "Texture_DifferenceEntropy_Actin_10_01_256"
## [217] "Texture_DifferenceEntropy_Actin_10_02_256"
## [218] "Texture_DifferenceEntropy_Actin_10_03_256"
## [219] "Texture_DifferenceEntropy_Actin_20_00_256"
## [220] "Texture_DifferenceEntropy_Actin_20_01_256"
## [221] "Texture_DifferenceEntropy_Actin_20_02_256"
## [222] "Texture_DifferenceEntropy_Actin_20_03_256"
## [223] "Texture_DifferenceEntropy_Actin_5_00_256"
## [224] "Texture_DifferenceEntropy_Actin_5_01_256"
## [225] "Texture_DifferenceEntropy_Actin_5_02_256"
## [226] "Texture_DifferenceEntropy_Actin_5_03_256"
## [227] "Texture_DifferenceVariance_Actin_10_00_256"
## [228] "Texture_DifferenceVariance_Actin_10_01_256"
## [229] "Texture_DifferenceVariance_Actin_10_02_256"
## [230] "Texture_DifferenceVariance_Actin_10_03_256"
## [231] "Texture_DifferenceVariance_Actin_20_00_256"
## [232] "Texture_DifferenceVariance_Actin_20_01_256"
## [233] "Texture_DifferenceVariance_Actin_20_02_256"
## [234] "Texture_DifferenceVariance_Actin_20_03_256"
## [235] "Texture_DifferenceVariance_Actin_5_00_256"
## [236] "Texture_DifferenceVariance_Actin_5_01_256"
## [237] "Texture_DifferenceVariance_Actin_5_02_256"
## [238] "Texture_DifferenceVariance_Actin_5_03_256"
## [239] "Texture_Entropy_Actin_10_00_256"
## [240] "Texture_Entropy_Actin_10_01_256"
## [241] "Texture_Entropy_Actin_10_02_256"
## [242] "Texture_Entropy_Actin_10_03_256"
## [243] "Texture_Entropy_Actin_20_00_256"
## [244] "Texture_Entropy_Actin_20_01_256"
## [245] "Texture_Entropy_Actin_20_02_256"
## [246] "Texture_Entropy_Actin_20_03_256"
## [247] "Texture_Entropy_Actin_5_00_256"
## [248] "Texture_Entropy_Actin_5_01_256"
## [249] "Texture_Entropy_Actin_5_02_256"
## [250] "Texture_Entropy_Actin_5_03_256"
## [251] "Texture_InfoMeas1_Actin_10_00_256"
## [252] "Texture_InfoMeas1_Actin_10_01_256"
## [253] "Texture_InfoMeas1_Actin_10_02_256"
## [254] "Texture_InfoMeas1_Actin_10_03_256"
## [255] "Texture_InfoMeas1_Actin_20_00_256"
## [256] "Texture_InfoMeas1_Actin_20_01_256"
## [257] "Texture_InfoMeas1_Actin_20_02_256"
## [258] "Texture_InfoMeas1_Actin_20_03_256"
## [259] "Texture_InfoMeas1_Actin_5_00_256"
## [260] "Texture_InfoMeas1_Actin_5_01_256"
## [261] "Texture_InfoMeas1_Actin_5_02_256"
## [262] "Texture_InfoMeas1_Actin_5_03_256"
## [263] "Texture_InfoMeas2_Actin_10_00_256"
## [264] "Texture_InfoMeas2_Actin_10_01_256"
## [265] "Texture_InfoMeas2_Actin_10_02_256"
## [266] "Texture_InfoMeas2_Actin_10_03_256"
## [267] "Texture_InfoMeas2_Actin_20_00_256"
## [268] "Texture_InfoMeas2_Actin_20_01_256"
## [269] "Texture_InfoMeas2_Actin_20_02_256"
## [270] "Texture_InfoMeas2_Actin_20_03_256"
## [271] "Texture_InfoMeas2_Actin_5_00_256"
## [272] "Texture_InfoMeas2_Actin_5_01_256"
## [273] "Texture_InfoMeas2_Actin_5_02_256"
## [274] "Texture_InfoMeas2_Actin_5_03_256"
## [275] "Texture_InverseDifferenceMoment_Actin_10_00_256"
## [276] "Texture_InverseDifferenceMoment_Actin_10_01_256"
## [277] "Texture_InverseDifferenceMoment_Actin_10_02_256"
## [278] "Texture_InverseDifferenceMoment_Actin_10_03_256"
## [279] "Texture_InverseDifferenceMoment_Actin_20_00_256"
## [280] "Texture_InverseDifferenceMoment_Actin_20_01_256"
## [281] "Texture_InverseDifferenceMoment_Actin_20_02_256"
## [282] "Texture_InverseDifferenceMoment_Actin_20_03_256"
## [283] "Texture_InverseDifferenceMoment_Actin_5_00_256"
## [284] "Texture_InverseDifferenceMoment_Actin_5_01_256"
## [285] "Texture_InverseDifferenceMoment_Actin_5_02_256"
## [286] "Texture_InverseDifferenceMoment_Actin_5_03_256"
## [287] "Texture_SumAverage_Actin_10_00_256"
## [288] "Texture_SumAverage_Actin_10_01_256"
## [289] "Texture_SumAverage_Actin_10_02_256"
## [290] "Texture_SumAverage_Actin_10_03_256"
## [291] "Texture_SumAverage_Actin_20_00_256"
## [292] "Texture_SumAverage_Actin_20_01_256"
## [293] "Texture_SumAverage_Actin_20_02_256"
## [294] "Texture_SumAverage_Actin_20_03_256"
## [295] "Texture_SumAverage_Actin_5_00_256"
## [296] "Texture_SumAverage_Actin_5_01_256"
## [297] "Texture_SumAverage_Actin_5_02_256"
## [298] "Texture_SumAverage_Actin_5_03_256"
## [299] "Texture_SumEntropy_Actin_10_00_256"
## [300] "Texture_SumEntropy_Actin_10_01_256"
## [301] "Texture_SumEntropy_Actin_10_02_256"
## [302] "Texture_SumEntropy_Actin_10_03_256"
## [303] "Texture_SumEntropy_Actin_20_00_256"
## [304] "Texture_SumEntropy_Actin_20_01_256"
## [305] "Texture_SumEntropy_Actin_20_02_256"
## [306] "Texture_SumEntropy_Actin_20_03_256"
## [307] "Texture_SumEntropy_Actin_5_00_256"
## [308] "Texture_SumEntropy_Actin_5_01_256"
## [309] "Texture_SumEntropy_Actin_5_02_256"
## [310] "Texture_SumEntropy_Actin_5_03_256"
## [311] "Texture_SumVariance_Actin_10_00_256"
## [312] "Texture_SumVariance_Actin_10_01_256"
## [313] "Texture_SumVariance_Actin_10_02_256"
## [314] "Texture_SumVariance_Actin_10_03_256"
## [315] "Texture_SumVariance_Actin_20_00_256"
## [316] "Texture_SumVariance_Actin_20_01_256"
## [317] "Texture_SumVariance_Actin_20_02_256"
## [318] "Texture_SumVariance_Actin_20_03_256"
## [319] "Texture_SumVariance_Actin_5_00_256"
## [320] "Texture_SumVariance_Actin_5_01_256"
## [321] "Texture_SumVariance_Actin_5_02_256"
## [322] "Texture_SumVariance_Actin_5_03_256"
## [323] "Texture_Variance_Actin_10_00_256"
## [324] "Texture_Variance_Actin_10_01_256"
## [325] "Texture_Variance_Actin_10_02_256"
## [326] "Texture_Variance_Actin_10_03_256"
## [327] "Texture_Variance_Actin_20_00_256"
## [328] "Texture_Variance_Actin_20_01_256"
## [329] "Texture_Variance_Actin_20_02_256"
## [330] "Texture_Variance_Actin_20_03_256"
## [331] "Texture_Variance_Actin_5_00_256"
## [332] "Texture_Variance_Actin_5_01_256"
## [333] "Texture_Variance_Actin_5_02_256"
## [334] "Texture_Variance_Actin_5_03_256"
# remove the redundant _Actin ...
object <-
renameTracksDfWith(
object = object,
.fn = ~ str_remove_all(.x, pattern = "_Actin"),
# ... only from variables that start with Intensity or RadialDistribution
.cols = starts_with(c("Intensity", "RadialDistribution"))
)
getTrackVariableNames(object)output
## [1] "Area"
## [2] "AS_BoundingBoxArea"
## [3] "AS_BoundingBoxMaximum_X"
## [4] "AS_BoundingBoxMaximum_Y"
## [5] "AS_BoundingBoxMinimum_X"
## [6] "AS_BoundingBoxMinimum_Y"
## [7] "AS_Center_X"
## [8] "AS_Center_Y"
## [9] "AS_Compactness"
## [10] "AS_Eccentricity"
## [11] "AS_EquivalentDiameter"
## [12] "AS_EulerNumber"
## [13] "AS_Extent"
## [14] "AS_FormFactor"
## [15] "AS_MajorAxisLength"
## [16] "AS_MaxFeretDiameter"
## [17] "AS_MaximumRadius"
## [18] "AS_MeanRadius"
## [19] "AS_MedianRadius"
## [20] "AS_MinFeretDiameter"
## [21] "AS_MinorAxisLength"
## [22] "AS_Orientation"
## [23] "AS_Perimeter"
## [24] "AS_Solidity"
## [25] "AS_Zernike_0_0"
## [26] "AS_Zernike_1_1"
## [27] "AS_Zernike_2_0"
## [28] "AS_Zernike_2_2"
## [29] "AS_Zernike_3_1"
## [30] "AS_Zernike_3_3"
## [31] "AS_Zernike_4_0"
## [32] "AS_Zernike_4_2"
## [33] "AS_Zernike_4_4"
## [34] "AS_Zernike_5_1"
## [35] "AS_Zernike_5_3"
## [36] "AS_Zernike_5_5"
## [37] "AS_Zernike_6_0"
## [38] "AS_Zernike_6_2"
## [39] "AS_Zernike_6_4"
## [40] "AS_Zernike_6_6"
## [41] "AS_Zernike_7_1"
## [42] "AS_Zernike_7_3"
## [43] "AS_Zernike_7_5"
## [44] "AS_Zernike_7_7"
## [45] "AS_Zernike_8_0"
## [46] "AS_Zernike_8_2"
## [47] "AS_Zernike_8_4"
## [48] "AS_Zernike_8_6"
## [49] "AS_Zernike_8_8"
## [50] "AS_Zernike_9_1"
## [51] "AS_Zernike_9_3"
## [52] "AS_Zernike_9_5"
## [53] "AS_Zernike_9_7"
## [54] "AS_Zernike_9_9"
## [55] "Children_Cytoplasm_Count"
## [56] "Granularity_10_Actin"
## [57] "Granularity_11_Actin"
## [58] "Granularity_12_Actin"
## [59] "Granularity_13_Actin"
## [60] "Granularity_14_Actin"
## [61] "Granularity_15_Actin"
## [62] "Granularity_16_Actin"
## [63] "Granularity_1_Actin"
## [64] "Granularity_2_Actin"
## [65] "Granularity_3_Actin"
## [66] "Granularity_4_Actin"
## [67] "Granularity_5_Actin"
## [68] "Granularity_6_Actin"
## [69] "Granularity_7_Actin"
## [70] "Granularity_8_Actin"
## [71] "Granularity_9_Actin"
## [72] "Intensity_IntegratedIntensityEdge"
## [73] "Intensity_IntegratedIntensity"
## [74] "Intensity_LowerQuartileIntensity"
## [75] "Intensity_MADIntensity"
## [76] "Intensity_MassDisplacement"
## [77] "Intensity_MaxIntensityEdge"
## [78] "Intensity_MaxIntensity"
## [79] "Intensity_MeanIntensityEdge"
## [80] "Intensity_MeanIntensity"
## [81] "Intensity_MedianIntensity"
## [82] "Intensity_MinIntensityEdge"
## [83] "Intensity_MinIntensity"
## [84] "Intensity_StdIntensityEdge"
## [85] "Intensity_StdIntensity"
## [86] "Intensity_UpperQuartileIntensity"
## [87] "Location_CenterMassIntensity_X_Actin"
## [88] "Location_CenterMassIntensity_Y_Actin"
## [89] "Location_MaxIntensity_X_Actin"
## [90] "Location_MaxIntensity_Y_Actin"
## [91] "Neighbors_AngleBetweenNeighbors_10"
## [92] "Neighbors_AngleBetweenNeighbors_Adjacent"
## [93] "Neighbors_FirstClosestDistance_10"
## [94] "Neighbors_FirstClosestDistance_Adjacent"
## [95] "Neighbors_FirstClosestObjectNumber_10"
## [96] "Neighbors_FirstClosestObjectNumber_Adjacent"
## [97] "Neighbors_NumberOfNeighbors_10"
## [98] "Neighbors_NumberOfNeighbors_Adjacent"
## [99] "Neighbors_PercentTouching_10"
## [100] "Neighbors_PercentTouching_Adjacent"
## [101] "Neighbors_SecondClosestDistance_10"
## [102] "Neighbors_SecondClosestDistance_Adjacent"
## [103] "Neighbors_SecondClosestObjectNumber_10"
## [104] "Neighbors_SecondClosestObjectNumber_Adjacent"
## [105] "Number_Object_Number"
## [106] "Parent_Nuclei"
## [107] "RadialDistribution_FracAtD_1of4"
## [108] "RadialDistribution_FracAtD_2of4"
## [109] "RadialDistribution_FracAtD_3of4"
## [110] "RadialDistribution_FracAtD_4of4"
## [111] "RadialDistribution_MeanFrac_1of4"
## [112] "RadialDistribution_MeanFrac_2of4"
## [113] "RadialDistribution_MeanFrac_3of4"
## [114] "RadialDistribution_MeanFrac_4of4"
## [115] "RadialDistribution_RadialCV_1of4"
## [116] "RadialDistribution_RadialCV_2of4"
## [117] "RadialDistribution_RadialCV_3of4"
## [118] "RadialDistribution_RadialCV_4of4"
## [119] "RadialDistribution_ZernikeMagnitude_0_0"
## [120] "RadialDistribution_ZernikeMagnitude_1_1"
## [121] "RadialDistribution_ZernikeMagnitude_2_0"
## [122] "RadialDistribution_ZernikeMagnitude_2_2"
## [123] "RadialDistribution_ZernikeMagnitude_3_1"
## [124] "RadialDistribution_ZernikeMagnitude_3_3"
## [125] "RadialDistribution_ZernikeMagnitude_4_0"
## [126] "RadialDistribution_ZernikeMagnitude_4_2"
## [127] "RadialDistribution_ZernikeMagnitude_4_4"
## [128] "RadialDistribution_ZernikeMagnitude_5_1"
## [129] "RadialDistribution_ZernikeMagnitude_5_3"
## [130] "RadialDistribution_ZernikeMagnitude_5_5"
## [131] "RadialDistribution_ZernikeMagnitude_6_0"
## [132] "RadialDistribution_ZernikeMagnitude_6_2"
## [133] "RadialDistribution_ZernikeMagnitude_6_4"
## [134] "RadialDistribution_ZernikeMagnitude_6_6"
## [135] "RadialDistribution_ZernikeMagnitude_7_1"
## [136] "RadialDistribution_ZernikeMagnitude_7_3"
## [137] "RadialDistribution_ZernikeMagnitude_7_5"
## [138] "RadialDistribution_ZernikeMagnitude_7_7"
## [139] "RadialDistribution_ZernikeMagnitude_8_0"
## [140] "RadialDistribution_ZernikeMagnitude_8_2"
## [141] "RadialDistribution_ZernikeMagnitude_8_4"
## [142] "RadialDistribution_ZernikeMagnitude_8_6"
## [143] "RadialDistribution_ZernikeMagnitude_8_8"
## [144] "RadialDistribution_ZernikeMagnitude_9_1"
## [145] "RadialDistribution_ZernikeMagnitude_9_3"
## [146] "RadialDistribution_ZernikeMagnitude_9_5"
## [147] "RadialDistribution_ZernikeMagnitude_9_7"
## [148] "RadialDistribution_ZernikeMagnitude_9_9"
## [149] "RadialDistribution_ZernikePhase_0_0"
## [150] "RadialDistribution_ZernikePhase_1_1"
## [151] "RadialDistribution_ZernikePhase_2_0"
## [152] "RadialDistribution_ZernikePhase_2_2"
## [153] "RadialDistribution_ZernikePhase_3_1"
## [154] "RadialDistribution_ZernikePhase_3_3"
## [155] "RadialDistribution_ZernikePhase_4_0"
## [156] "RadialDistribution_ZernikePhase_4_2"
## [157] "RadialDistribution_ZernikePhase_4_4"
## [158] "RadialDistribution_ZernikePhase_5_1"
## [159] "RadialDistribution_ZernikePhase_5_3"
## [160] "RadialDistribution_ZernikePhase_5_5"
## [161] "RadialDistribution_ZernikePhase_6_0"
## [162] "RadialDistribution_ZernikePhase_6_2"
## [163] "RadialDistribution_ZernikePhase_6_4"
## [164] "RadialDistribution_ZernikePhase_6_6"
## [165] "RadialDistribution_ZernikePhase_7_1"
## [166] "RadialDistribution_ZernikePhase_7_3"
## [167] "RadialDistribution_ZernikePhase_7_5"
## [168] "RadialDistribution_ZernikePhase_7_7"
## [169] "RadialDistribution_ZernikePhase_8_0"
## [170] "RadialDistribution_ZernikePhase_8_2"
## [171] "RadialDistribution_ZernikePhase_8_4"
## [172] "RadialDistribution_ZernikePhase_8_6"
## [173] "RadialDistribution_ZernikePhase_8_8"
## [174] "RadialDistribution_ZernikePhase_9_1"
## [175] "RadialDistribution_ZernikePhase_9_3"
## [176] "RadialDistribution_ZernikePhase_9_5"
## [177] "RadialDistribution_ZernikePhase_9_7"
## [178] "RadialDistribution_ZernikePhase_9_9"
## [179] "Texture_AngularSecondMoment_Actin_10_00_256"
## [180] "Texture_AngularSecondMoment_Actin_10_01_256"
## [181] "Texture_AngularSecondMoment_Actin_10_02_256"
## [182] "Texture_AngularSecondMoment_Actin_10_03_256"
## [183] "Texture_AngularSecondMoment_Actin_20_00_256"
## [184] "Texture_AngularSecondMoment_Actin_20_01_256"
## [185] "Texture_AngularSecondMoment_Actin_20_02_256"
## [186] "Texture_AngularSecondMoment_Actin_20_03_256"
## [187] "Texture_AngularSecondMoment_Actin_5_00_256"
## [188] "Texture_AngularSecondMoment_Actin_5_01_256"
## [189] "Texture_AngularSecondMoment_Actin_5_02_256"
## [190] "Texture_AngularSecondMoment_Actin_5_03_256"
## [191] "Texture_Contrast_Actin_10_00_256"
## [192] "Texture_Contrast_Actin_10_01_256"
## [193] "Texture_Contrast_Actin_10_02_256"
## [194] "Texture_Contrast_Actin_10_03_256"
## [195] "Texture_Contrast_Actin_20_00_256"
## [196] "Texture_Contrast_Actin_20_01_256"
## [197] "Texture_Contrast_Actin_20_02_256"
## [198] "Texture_Contrast_Actin_20_03_256"
## [199] "Texture_Contrast_Actin_5_00_256"
## [200] "Texture_Contrast_Actin_5_01_256"
## [201] "Texture_Contrast_Actin_5_02_256"
## [202] "Texture_Contrast_Actin_5_03_256"
## [203] "Texture_Correlation_Actin_10_00_256"
## [204] "Texture_Correlation_Actin_10_01_256"
## [205] "Texture_Correlation_Actin_10_02_256"
## [206] "Texture_Correlation_Actin_10_03_256"
## [207] "Texture_Correlation_Actin_20_00_256"
## [208] "Texture_Correlation_Actin_20_01_256"
## [209] "Texture_Correlation_Actin_20_02_256"
## [210] "Texture_Correlation_Actin_20_03_256"
## [211] "Texture_Correlation_Actin_5_00_256"
## [212] "Texture_Correlation_Actin_5_01_256"
## [213] "Texture_Correlation_Actin_5_02_256"
## [214] "Texture_Correlation_Actin_5_03_256"
## [215] "Texture_DifferenceEntropy_Actin_10_00_256"
## [216] "Texture_DifferenceEntropy_Actin_10_01_256"
## [217] "Texture_DifferenceEntropy_Actin_10_02_256"
## [218] "Texture_DifferenceEntropy_Actin_10_03_256"
## [219] "Texture_DifferenceEntropy_Actin_20_00_256"
## [220] "Texture_DifferenceEntropy_Actin_20_01_256"
## [221] "Texture_DifferenceEntropy_Actin_20_02_256"
## [222] "Texture_DifferenceEntropy_Actin_20_03_256"
## [223] "Texture_DifferenceEntropy_Actin_5_00_256"
## [224] "Texture_DifferenceEntropy_Actin_5_01_256"
## [225] "Texture_DifferenceEntropy_Actin_5_02_256"
## [226] "Texture_DifferenceEntropy_Actin_5_03_256"
## [227] "Texture_DifferenceVariance_Actin_10_00_256"
## [228] "Texture_DifferenceVariance_Actin_10_01_256"
## [229] "Texture_DifferenceVariance_Actin_10_02_256"
## [230] "Texture_DifferenceVariance_Actin_10_03_256"
## [231] "Texture_DifferenceVariance_Actin_20_00_256"
## [232] "Texture_DifferenceVariance_Actin_20_01_256"
## [233] "Texture_DifferenceVariance_Actin_20_02_256"
## [234] "Texture_DifferenceVariance_Actin_20_03_256"
## [235] "Texture_DifferenceVariance_Actin_5_00_256"
## [236] "Texture_DifferenceVariance_Actin_5_01_256"
## [237] "Texture_DifferenceVariance_Actin_5_02_256"
## [238] "Texture_DifferenceVariance_Actin_5_03_256"
## [239] "Texture_Entropy_Actin_10_00_256"
## [240] "Texture_Entropy_Actin_10_01_256"
## [241] "Texture_Entropy_Actin_10_02_256"
## [242] "Texture_Entropy_Actin_10_03_256"
## [243] "Texture_Entropy_Actin_20_00_256"
## [244] "Texture_Entropy_Actin_20_01_256"
## [245] "Texture_Entropy_Actin_20_02_256"
## [246] "Texture_Entropy_Actin_20_03_256"
## [247] "Texture_Entropy_Actin_5_00_256"
## [248] "Texture_Entropy_Actin_5_01_256"
## [249] "Texture_Entropy_Actin_5_02_256"
## [250] "Texture_Entropy_Actin_5_03_256"
## [251] "Texture_InfoMeas1_Actin_10_00_256"
## [252] "Texture_InfoMeas1_Actin_10_01_256"
## [253] "Texture_InfoMeas1_Actin_10_02_256"
## [254] "Texture_InfoMeas1_Actin_10_03_256"
## [255] "Texture_InfoMeas1_Actin_20_00_256"
## [256] "Texture_InfoMeas1_Actin_20_01_256"
## [257] "Texture_InfoMeas1_Actin_20_02_256"
## [258] "Texture_InfoMeas1_Actin_20_03_256"
## [259] "Texture_InfoMeas1_Actin_5_00_256"
## [260] "Texture_InfoMeas1_Actin_5_01_256"
## [261] "Texture_InfoMeas1_Actin_5_02_256"
## [262] "Texture_InfoMeas1_Actin_5_03_256"
## [263] "Texture_InfoMeas2_Actin_10_00_256"
## [264] "Texture_InfoMeas2_Actin_10_01_256"
## [265] "Texture_InfoMeas2_Actin_10_02_256"
## [266] "Texture_InfoMeas2_Actin_10_03_256"
## [267] "Texture_InfoMeas2_Actin_20_00_256"
## [268] "Texture_InfoMeas2_Actin_20_01_256"
## [269] "Texture_InfoMeas2_Actin_20_02_256"
## [270] "Texture_InfoMeas2_Actin_20_03_256"
## [271] "Texture_InfoMeas2_Actin_5_00_256"
## [272] "Texture_InfoMeas2_Actin_5_01_256"
## [273] "Texture_InfoMeas2_Actin_5_02_256"
## [274] "Texture_InfoMeas2_Actin_5_03_256"
## [275] "Texture_InverseDifferenceMoment_Actin_10_00_256"
## [276] "Texture_InverseDifferenceMoment_Actin_10_01_256"
## [277] "Texture_InverseDifferenceMoment_Actin_10_02_256"
## [278] "Texture_InverseDifferenceMoment_Actin_10_03_256"
## [279] "Texture_InverseDifferenceMoment_Actin_20_00_256"
## [280] "Texture_InverseDifferenceMoment_Actin_20_01_256"
## [281] "Texture_InverseDifferenceMoment_Actin_20_02_256"
## [282] "Texture_InverseDifferenceMoment_Actin_20_03_256"
## [283] "Texture_InverseDifferenceMoment_Actin_5_00_256"
## [284] "Texture_InverseDifferenceMoment_Actin_5_01_256"
## [285] "Texture_InverseDifferenceMoment_Actin_5_02_256"
## [286] "Texture_InverseDifferenceMoment_Actin_5_03_256"
## [287] "Texture_SumAverage_Actin_10_00_256"
## [288] "Texture_SumAverage_Actin_10_01_256"
## [289] "Texture_SumAverage_Actin_10_02_256"
## [290] "Texture_SumAverage_Actin_10_03_256"
## [291] "Texture_SumAverage_Actin_20_00_256"
## [292] "Texture_SumAverage_Actin_20_01_256"
## [293] "Texture_SumAverage_Actin_20_02_256"
## [294] "Texture_SumAverage_Actin_20_03_256"
## [295] "Texture_SumAverage_Actin_5_00_256"
## [296] "Texture_SumAverage_Actin_5_01_256"
## [297] "Texture_SumAverage_Actin_5_02_256"
## [298] "Texture_SumAverage_Actin_5_03_256"
## [299] "Texture_SumEntropy_Actin_10_00_256"
## [300] "Texture_SumEntropy_Actin_10_01_256"
## [301] "Texture_SumEntropy_Actin_10_02_256"
## [302] "Texture_SumEntropy_Actin_10_03_256"
## [303] "Texture_SumEntropy_Actin_20_00_256"
## [304] "Texture_SumEntropy_Actin_20_01_256"
## [305] "Texture_SumEntropy_Actin_20_02_256"
## [306] "Texture_SumEntropy_Actin_20_03_256"
## [307] "Texture_SumEntropy_Actin_5_00_256"
## [308] "Texture_SumEntropy_Actin_5_01_256"
## [309] "Texture_SumEntropy_Actin_5_02_256"
## [310] "Texture_SumEntropy_Actin_5_03_256"
## [311] "Texture_SumVariance_Actin_10_00_256"
## [312] "Texture_SumVariance_Actin_10_01_256"
## [313] "Texture_SumVariance_Actin_10_02_256"
## [314] "Texture_SumVariance_Actin_10_03_256"
## [315] "Texture_SumVariance_Actin_20_00_256"
## [316] "Texture_SumVariance_Actin_20_01_256"
## [317] "Texture_SumVariance_Actin_20_02_256"
## [318] "Texture_SumVariance_Actin_20_03_256"
## [319] "Texture_SumVariance_Actin_5_00_256"
## [320] "Texture_SumVariance_Actin_5_01_256"
## [321] "Texture_SumVariance_Actin_5_02_256"
## [322] "Texture_SumVariance_Actin_5_03_256"
## [323] "Texture_Variance_Actin_10_00_256"
## [324] "Texture_Variance_Actin_10_01_256"
## [325] "Texture_Variance_Actin_10_02_256"
## [326] "Texture_Variance_Actin_10_03_256"
## [327] "Texture_Variance_Actin_20_00_256"
## [328] "Texture_Variance_Actin_20_01_256"
## [329] "Texture_Variance_Actin_20_02_256"
## [330] "Texture_Variance_Actin_20_03_256"
## [331] "Texture_Variance_Actin_5_00_256"
## [332] "Texture_Variance_Actin_5_01_256"
## [333] "Texture_Variance_Actin_5_02_256"
## [334] "Texture_Variance_Actin_5_03_256"Renaming all other variables apart from protected ones like cell_id, condition or cell_line works in a similar fashion. Use renameMetaDf(), renameMetaDfWith(), renameClusterDf() and renameClusterDfWith() for that matter.
getClusterVariableNames(object)output
## [1] "hcl_euclidean_complete_k_3_(intensity)"
## [2] "hcl_euclidean_complete_k_4_(intensity)"
## [3] "hcl_euclidean_complete_k_5_(intensity)"
## [4] "hcl_euclidean_ward.D_k_3_(intensity)"
## [5] "hcl_euclidean_ward.D_k_4_(intensity)"
## [6] "hcl_euclidean_ward.D_k_5_(intensity)"
## [7] "kmeans_Lloyd_k_3_(intensity)"
## [8] "kmeans_Lloyd_k_4_(intensity)"
## [9] "kmeans_Lloyd_k_5_(intensity)"
## [10] "pam_euclidean_k_4_(intensity)"
## [11] "pam_euclidean_k_5_(intensity)"
# if only intensity based clustering results exist and you don't plan to add any more you might
# want to cut the suffix
object <-
renameClusterDfWith(
object = object,
.fn = ~ str_remove_all(.x, pattern = "_\\(intensity\\)")
)
getClusterVariableNames(object) output
## [1] "hcl_euclidean_complete_k_3" "hcl_euclidean_complete_k_4"
## [3] "hcl_euclidean_complete_k_5" "hcl_euclidean_ward.D_k_3"
## [5] "hcl_euclidean_ward.D_k_4" "hcl_euclidean_ward.D_k_5"
## [7] "kmeans_Lloyd_k_3" "kmeans_Lloyd_k_4"
## [9] "kmeans_Lloyd_k_5" "pam_euclidean_k_4"
## [11] "pam_euclidean_k_5"Group names are often suboptimal. For instance, clustering algorithms return numbers as names for cluster. This is rarely informative and if your analysis results in the identification of biologically meaningfully subgroups you might want to rename these groups accordingly. Use renameGroups() for that matter. It works with the same new_name = old_name syntax as the rename*() functions mentioned previously.
getGroupNames(object = object, grouping_variable = "pam_euclidean_k_4")output
## [1] "1" "2" "3" "4"
object <-
renameGroups(
object = object,
grouping_variable = "pam_euclidean_k_4",
"round_shape" = "1", # new_name = old_name
"long_shape" = "2",
"rectangular_like" = "3",
"triangular_like" = "4"
)
getGroupNames(object, grouping_variable = "pam_euclidean_k_4")output
## [1] "round_shape" "long_shape" "rectangular_like" "triangular_like"
getClusterDf(object) %>%
select(cell_id, pam_euclidean_k_4)output
## # A tibble: 13,000 x 2
## cell_id pam_euclidean_k_4
## <chr> <fct>
## 1 CID_1_WI_B10_1_WP_1 round_shape
## 2 CID_2_WI_B10_1_WP_1 round_shape
## 3 CID_7_WI_B10_1_WP_1 long_shape
## 4 CID_10_WI_B10_1_WP_1 round_shape
## 5 CID_14_WI_B10_1_WP_1 long_shape
## 6 CID_15_WI_B10_1_WP_1 round_shape
## 7 CID_17_WI_B10_1_WP_1 round_shape
## 8 CID_20_WI_B10_1_WP_1 long_shape
## 9 CID_21_WI_B10_1_WP_1 long_shape
## 10 CID_22_WI_B10_1_WP_1 round_shape
## # ... with 12,990 more rows