mrcImageClusterAnalysis

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mrcImageClusterAnalysis is Eos's Command that performs Cluster Analysis each mrcImage.


List of option

Main option

Option Essential/Optional Description Default
-I Essential Input: ASCII NULL
-o Optional Output: ASCII stdout
-O Optional Output(averaged images): filename: (Input file's name).avg
-N Optional Number of clusters 1
-Min Optional Minimum: Correlation: Conditions for ending 0.0
-Iter Optional IterationFlag
-AR Optional AutoRotation: rotation divided by this value 72
-ARange Optional AutoRotationRange: (ARMin, ARMax) (0, 360)
-ARiter Optional AutoRotationIteration 2
-ARMethod Optional Method for Correlation for Auto Rotation 0
-M Optional Correlation Mode for AutoRotation 19
-pvm Optional Parallel Analysis by PVM
-pvmList Optional Input: pvmList: ASCII NULL
-Log Optional Output: Log(All):ASCII stdout
-Log2 Optional Output: Log2(ClusterNode Only): ASCII NULL
-LogIn Optional Input: previousLog: ASCII NULL
-prevF Optional Input: previousLogFileNum 0
-c Optional ConfigurationFile NULL
-m Optional Mode of the distance between the clusters 2
-h Optional Help 　
-AR: Setting, calculated by the rotation there. (Using mrcImageAutoRotationCorrelation)


-ARMethod, -M details

cf mrcImageAutoRotationCorrelation
-ARMethod to -Method, -M to -m


-m details

Value Description
0 By Correlation
1 By Euclid Distance
2 By Ward Method: without -AR: Euclid Length, with -AR: its square
3 By Ward Method using Linear Correlation : (1 - Correlation)/(1 + Correlation)
4 By Linear Correlation : (1 - Correlation)/(1 + Correlation)


Execution example

-I data

Input-1VOM-N-2D.mrc
Input-1VOM-N-Rot-2D.mrc
Input-1VOM-N-Rot1-2D.mrc
Input-1VOM-N-Rot2-2D.mrc
Input-1VOM-N-Rot3-2D.mrc
Input-1VOM-N-2D.mrc's image
Input-1VOM-N-2D.png

Min

Max
Mean
SD

SE

-18651.7 (10, 1, 0)

52942.7 (24, 39, 0)
7214.87
10067.6

125.845
Input-1VOM-N-Rot-2D.mrc's image
Input-1VOM-N-Rot-2D.png

Min

Max
Mean
SD

SE

-11367.8 (51, 62, 0)

51939.8 (29, 26, 0)
6580.18
9247.8

115.597
Input-1VOM-N-Rot1-2D.mrc's image
Input-1VOM-N-Rot1-2D.png

Min

Max
Mean
SD

SE

-14918 (53, 17, 0)

58621.8 (30, 26, 0)
6579.96
9022.72

112.784
Input-1VOM-N-Rot2-2D.mrc's image
Input-1VOM-N-Rot2-2D.png

Min

Max
Mean
SD

SE

-2.31309e-06 (29, 7, 0)

49749.2 (52, 51, 0)
6572.32
8769.91

109.624
Input-N-1VOM-Rot3-2D.mrc's image
Input-1VOM-N-Rot3-2D.png

Min

Max
Mean
SD

SE

-1.70846e-06 (56, 57, 0)

40287.6 (43, 43, 0)
6509.38
8494.21

106.178


Example of options only essential

-o 's data
/Eos/Input-1VOM-N-2D.mrc 0
/Eos/Input-1VOM-N-Rot-2D.mrc 0
/Eos/Input-1VOM-N-Rot1-2D.mrc 0
/Eos/Input-1VOM-N-Rot2-2D.mrc 0
/Eos/Input-1VOM-N-Rot3-2D.mrc 0


-Log 's data
         1          0          5          5     4.24643e+11
         2          0          5          5     4.71782e+11
         2          1          5          5     2.57991e+11
         3          0          5          5     6.14144e+11
         3          1          5          5     4.54881e+11
         3          2          5          5      4.2017e+11
         4          0          5          5     6.53985e+11
         4          1          5          5     5.09646e+11
         4          2          5          5     4.66033e+11
         4          3          5          5     3.09305e+11
         1          0          2          1     3.83715e+11
         2          0          2          1     6.14144e+11
         2          1          2          1     3.73028e+11
         3          0          2          1     6.53985e+11
         3          1          2          1     4.23342e+11
         3          2          2          1     3.09305e+11
         1          0          3          2     3.83715e+11
         2          0          3          2     5.56738e+11
         2          1          3          2     3.20859e+11
         1          0          2          1     3.90012e+11


-Log2 's data
CLUST  MIN                 2     1     2.57991e+11               0
CLUST  MIN                 4     3     3.09305e+11               0
CLUST  MIN                 3     1     3.20859e+11               0
CLUST  MIN                 1     0     3.90012e+11               0


-O 's data
Input-1VOM-N-2D.mrc.avg
Outdata5-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-5026.5 (68, 63, 0)

28784 (40, 46, 0)
6685.03
7223.34

90.2917
Input-1VOM-N-Rot-2D.mrc.avg
Outdata6-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-5026.5 (68, 63, 0)

28784 (40, 46, 0)
6685.03
7223.34

90.2917
Input-1VOM-N-Rot1-2D.mrc.avg
Outdata7-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-8305.58 (63, 47, 0)

44934.5 (29, 26, 0)
6580.07
8566.67

107.083
Input-1VOM-N-Rot2-2D.mrc.avg
Outdata8-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-4662.21 (68, 63, 0)

32714.4 (21, 49, 0)
6552.58
7209.85

90.1231
Input-1VOM-N-Rot3-2D.mrc.avg
Outdata9-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-8070.97 (31, 10, 0)

39082.1 (53, 39, 0)
6525.08
7459.33

93.2416


Option -AR

Case: AR=72

-o 's data
/Eos/Input-1VOM-N-2D.mrc 0
/Eos/Input-1VOM-N-Rot-2D.mrc 0
/Eos/Input-1VOM-N-Rot1-2D.mrc 0
/Eos/Input-1VOM-N-Rot2-2D.mrc 0
/Eos/Input-1VOM-N-Rot3-2D.mrc 0


-Log 's data
         1          0          5          5     1.04435e+11
         2          0          5          5     1.90062e+11
         2          1          5          5     1.27924e+11
         3          0          5          5     2.70151e+11
         3          1          5          5     2.24399e+11
         3          2          5          5     2.00805e+11
         4          0          5          5     2.70277e+11
         4          1          5          5     2.23333e+11
         4          2          5          5     2.13958e+11
         4          3          5          5     1.54653e+11
         1          0          1          0     1.77375e+11
         2          0          1          0     2.92444e+11
         2          1          1          0     2.00805e+11
         3          0          1          0     2.95344e+11
         3          1          1          0     2.13958e+11
         3          2          1          0     1.54653e+11
         1          0          3          2     1.77375e+11
         2          0          3          2     3.71482e+11
         2          1          3          2     2.33577e+11
         1          0          1          0     3.72121e+11


-Log2 's data
CLUST  MIN                 1     0     1.04435e+11         0.83054
CLUST  MIN                 4     3     1.54653e+11        0.643245
CLUST  MIN                 2     0     1.77375e+11        0.751614
CLUST  MIN                 3     0     3.72121e+11        0.635649


-O 's data
Input-1VOM-N-2D.mrc.avg
Outdata-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-5248.9 (41, 3, 0)

37074.9 (26, 29, 0)
6687.62
7446.87

93.0859
Input-1VOM-N-Rot-2D.mrc.avg
Outdata1-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-11857.7 (56, 22, 0)

46633.1 (27, 28, 0)
6897.66
9242.12

115.527
Input-1VOM-N-Rot1-2D.mrc.avg
Outdata2-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-9406.5 (41, 3, 0)

50054.7 (27, 28, 0)
6792.38
8652.36

108.155
Input-1VOM-N-Rot2-2D.mrc.avg
Outdata3-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-5248.9 (41, 3, 0)

37074.9 (26, 29, 0)
6687.62
7446.87

93.0859
Input-1VOM-N-Rot3-2D.mrc.avg
Outdata4-mrcImageClusterAnalysis.png

Min

Max
Mean
SD

SE

-8070.97 (31, 10, 0)

39082.1 (53, 39, 0)
6525.08
7459.33

93.2416


Retrieved from "http://www.yasunaga-lab.bio.kyutech.ac.jp/Eos/index.php?title=mrcImageClusterAnalysis&oldid=3441"