forked from cran/WGCNA
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathChangelog
2092 lines (1450 loc) · 75.7 KB
/
Changelog
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
Note: as of 2009/03/10, changes that lead to different calculational results are marked as DIFF.
2023/01/07: 1.72
. Version bump for release
2022/12/29: 1.71-7
. Small changes in default position of legend label in labeledHeatmap
. C code reorganized to conform to the requirement of declaring all
function prototypes before definition
. Fixed version numbers in changelog.
2022/11/01: 1.71-6
. Bugfix in modulePreservation fixes checking for testNetworks out of
range. The bug made no difference for valid inputs.
2022/10/24: 1.71-5
. Function overlapTable nwo also returns a matrix of expected overlap
counts and a matrix of ratios of observed and expected overlap
counts.
. Bugfix in individualTOMs that fixes a crash in
hierarchicalConsensusModules when networkOptions are given as a
single object of class networkOptions.
. Internal functions for creating heatmaps with legend are improved.
2022/09/14: 1.71-4
. Function overlapTable now optionally returns logarithms of the
overlap p-values.
2022/07/03: 1.71-3
. Function prependZeros now gets the number of characters correctly
even for numbers like 100000 which were previously formatted to
1e05.
2022/07/02: 1.71-2
. Functions matchLabels and overlapTable now work also in the case
where one set of labels consists entirely of ignored labels.
. Function imputeByModule only imputes data in those modules that
actually contain missing data.
2022/05/22: 1.71-1
. empiricalBayesLM is a bit informative about failed initial
regressions.
2022/04/22: 1.71
. Version bumb for release
2022/04/08: 1.70-80
. Bugfix in blueWhiteRed and greenWhiteRed that makes the pallettes
symmetric for small odd values of n.
. Function sampleModules now runs nRuns sampled calculations (and
optionally also the unsampled calculation) rather than always
running precisely nRuns calculations.
. Function blueWhiteRed now accepts arguments giving the blue end, red
end and middle colors.
. Fixed bug in positioning color legend label for labeledHeatmap and
related functions.
. verboseIplot now accepts argument showMSE that can supress printing
of MSE in the title of the plot.
. verboseScatterplot now accepts argument showPValue that can suppress
printing of the p-value in the title of the plot.
. addGrid now accepts arguments linesPerTick.horiz and
linesPerTick.vert allowing the user to set the number of lines per
tick separately for the vertical and horizontal lines
. empiricalBayesLM now accepts argument scaleMeansOfSamples that works
in conjunction with scaleMeansToSamples to fine tune how the
adjustment is applied.
2021/03/01: 1.70-4
. plotColorUnderTree and plotDendroAndColor now work also when there
the 'colors' argument has length zero, producing an empty color
plot.
. Improvements in internal code plotting legends for labeledHeatmap.
2021/02/17: 1.70-3:
. Bugfixes of bugs introduced in 1.70-2
2021/02/13: 1.70-2:
. Fixed problem in moduleEigengenes with argument 'expr' not having
'rownames'.
2021/02/13: 1.70-1:
. Fixed several old web links in help files
2021/02/10: 1.69-86, 1.70
. Internal code for generating axis ticks now works when the limits
have zero range.
. Help files for blockwiseIndividualTOMs and blockwiseConsensusModules
updated.
2020/12/18: 1.69-85
. Internal code for plotting legends for heatmaps expanded to be able
to plot several color columns per legend.
2020/11/03: 1.69-84
. Internal code for plotting color scale/axis for heatmaps can now add
an axis label.
. Corrected help files.
2020/07/12: 1.69-83:
. Code for labeledHeatmap.multipage was simplified by taking advantage
of arguments showRows and showCols to labeledHeatmap. This also
solves incorrect font size and colors for the row and column labels.
2020/05/08: 1.69-82:
. blockwiseConsensusModules and friends now use make.unique before
assigning rownames, to guard against duplicate rownames errors.
2020/04/30: 1.69-81
. Bugfix in internal code fixes failure of labeledHeatmap with only
one column or row.
2020/03/03: 1.69-80
. Minor enhancements in internal code (function
.plotOrderedColorSubplot).
2020/02/28: 1.68-86, 1.69
. Argument nameOut to userListEnrichment now accepts value NULL to
suppress generating a file with the results.
. lmRob has been removed as an automatically supported optional
initial fit function in empiricalBayesLM (due to the package
'robust' having been orphaned and archived on CRAN).
. labeledHeatmap and internal function heatmapWithLegend now take
optional argument colorMat allowing the user to specify the cell
colors explicitly.
. Internal function heatmapWithLegend shoudl be able to use handle
transparent as color for missing data.
. Bugfix in internal function used in plotColorUnderTree and
plotOrderedColor.
2020/02/08: 1.68-84
. Further bugfixes in plotOrderedColor.
2020/02/06: 1.68-83
. plotOrderedColors, plotColorUnderTree and plotDendroAndColors gain argument
separatorLine.col to set (or omit) separator lines between color
rows.
. plotOrderedColors also gains argument align to provide some degree
of control over alignment of color rectangles.
2020/02/03: 1.68-82
. Bugfixes in prependZeros and internal code
(.boxDimensionsForHeatmapWithLegend).
. Internal change: plotOrderedColor is now split into user-facing
wrapper and the workhorse internal function that can be called from
other functions as well.
. Internal change: split off labeledHeatmap into is own file.
. prependZeros now handles fractional numbers better.
. goodSamplesMS and goodSamplesGenesMS now copy the 'names' attribute
of the input 'multiExpr' to the output.
. Function hierarchicalConsensusModules and
pruneAndMergeConsensusModules now calculate eigengenes with more
regard to resource utilization, skipping the some unneeded
calcualtions.
. Bugfix in labeledHeatmap and related functions; showing two
separators at the same position now works.
. metaAnalysis now works with a single data set.
. Example for chooseTopHubInEachModule has been simplified.
. DIFF: Argument scaleMeanToSamples for function empiricalBayesLM now
defaults to fitToSamples. This will produce adjusted data wwith
different means than before if non-trivial fitToSamples is used.
(The variation of the adjusted data is unchanged, i.e., correlations
of the adjusted data will be the same as before.) To reproduce old
results, use scaleMeanToSamples = NULL when calling empiricalBayesLM.
2019/06/18: 1.68-80
. binarizeCategoricalColumns.forPlots now accepts argument checkNames.
2019/06/02: 1.68-2
. Internal code checking and scaling multiData weights is now more
general.
2019/05/30: 1.68-1
. Function matchLabels is now nearly two orders of magnitude faster.
. Bugfix in sizeRestrictedClusterMerge fizes an error that ocurred
when some clusters were of size 1
2019/05/22: 1.68
. Bugfix in sizeRestrictedClusterMerge which also benefits
projectiveKMeans and blockwiseModules fixes an occasional crash.
Bug reports and assistance of several users, especially Luis Revilla,
is gratefully acknowledged.
. Bugfixes in blockwiseModules, blockwiseConsensusModules and
individualTOMs fix non-propagation of randomSeed to
projectiveKMeans. The default randomSeed for the 3 functions has
changed to match that of projectiveKMeans and
consensusProjectiveKMeans to make previous results reproducible.
. plotOrderedColor now returns some of the plotting information,
useful for adding to the plot.
. modulePreservation gains arguments multiWeights representing
optional observation weights of expression data, and goldName that
can be used to change the label used for all-network sample.
. Adding arguments horizontalSeparator.interval and
verticalSeparator.interval to labeledHeatmap
. Change in sampledHierarchicalModules: saveIndividualTOMs and
saveConsensusTOM arguments for the underlying
hierarchicalConsensusModules can be set as arguments rather than
being hardcoded.
2019/05/05: 1.67-90
. Bugfix in sizeRestrictedClusterMerge and projectiveKMeans that calls
it fixes occassional crash (reported on Stackexchange by user holly)
. Bugfix in modulePreservation: empty rownames of certain
matrices do not cause a crash anymore.
. New (experimental) versions of Topological Overlap (TOM) are
available.
. bugfix in exportNetworkToVisANT thanks to Guangjian Du
. consensusProjectiveKMeans is a bit more efficient, especially when
the number of sets is 1.
. goodGenes should be faster when weights are not supplied
2019/04/11: 1.67
. moduleEigengenes and derived functions (multiSetMEs) now copy
row names of the input data as row names of the output matrices.
. blockwiseModules, blockwiseConsensusModules, their 'recut' versions
and blockwiseHierarchicalModules now copy the column names of input
data into names of output module labels and colors. Row names of
input data are copied into row names of the corresponding module
eigengene matrices.
. Startup message regarding setting up multi-threading is now
disabled.
2019/04/09: 1.66-92
. bugfix in labeledHeatmap makes vertical separator lines better
aligned with standard position of labels.
. exportNetworkToCytoscape does not check column names in nodeAttr for
being valid language names.
2019/02/25: 1.66-90
. Bugfix in consensusTOM: saving calibrated TOMs should work now.
. Function formatLabels now accepts optional argument font.
. Function hierarchicalConsensusKME now accepts argument
getMetaColsFor1Set that controls whether meta-statistics are
returned when the consensus only has 1 input set.
. One more bugfix in internal code (.interleave)
. Bugfix in internal code (.interleave) fixes crashes in
hierarchicalConsensusKME
. Bugfix in multiGrep fixes sorting order when returning values rather
than indices.
. Functions consensusKME and hierachicalConsensusKME now don't throw
an error on duplicate column names in input data.
. Changed default for argument saveConsensusData from TRUE to NULL
(automatically determined from input data) in function
consensusCalculation
. Signed TOM described by Nowick et al (PNAS, 2009) is implemented and
can be accessed using TOMType = "signed Nowick" for all TOM
calculation and module identification functions that take argument
TOMType. Argument suppressNegativeTOM can be used to automatically
set all negative TOM values to zero.
. New argument suppressNegativeResults for newConsensusOptions.
. New function sizeRestrictedClusterMerge for merging clusters such
that the resulting clusters do not exceed a specified size.
. hierarchicalConsensusKME is now more robust and works with a single
module as well.
2018/10/22: 1.66
. Function consensusDissTOMandTree is now a it faster because of more
efficient garbage collection.
. Function verboseBarplot can now optionally add text labels to the
(also optional) scatterplot.
. In internal functions plotting heatmap legends, widths are now
specified in inches rather than in user coordinates.
. Hierarchical consensus module merging is now more robust to unusual
cases with 0 or only 1 module.
. Bugfix in hierarchicalConsensusModules: supplying a single
networkOptions dows not produce an error.
. pruneAndMergeConsensusModules now checks for presence of at least
one module; if no modules are present, it returns the input labels
rather than throwing an error.
. DIFF: Bugfix in hierarchicalConsensusModules changes the order of
imputation and removal of genes and samples with too many missing
values. This may lead to slightly different module eigengenes.
2018/10/02: 1.65
. Bugfix in modulePreservation fixes duplicate rownames error.
. Function signedKME now checks that colnames of the input data are
unique and makes them unique if not.
. Consensus calculations now return origin count for all consensus
quantiles and the mean consensus. Origin count for each set is the
number of (calibrated) values from the set that are less than or equal
the consensus.
. New function consensusTreeInputs for getting inputs of a consensus
tree.
2018/09/24: 1.64-81
. Fixed crash in softConnectivity when weights are used.
. Fixed bug in labeledHeatmap that transposed a 1-row matrix into a
1-column one.
. Fixed minor typos in errors emitted by labeledHeatmap.
2018/09/14: 1.64-80
. empiricalBayesLM now accepts optional argument fitToSamples that can
restrict the fitting process to a subset of samples. The argument
order was also rearranged to make the order more logical.
2018/09/09: 1.64-1
. binarizeCategoricalColumns.for... have re-ordered and in some cases
added arguments to make them more useful.
2018/09/05: 1.64
. Web site link updated
. Documentation for cor has been improved by making more precise what
nThreads actually affects
. Documentation for pickSoftThreshold.fromSimilarity has been improved
thanks to a suggestion from Paolo Inglese.
. Function signedKME has been streamlined and a bug in which gene
names in the output were passed through check.names in coercing the
input to a data frmae is now fixed.
. New functions binarizeCategoricalVariable,
binarizeCategoricalColumns, and related wrappers for binarizing
categorical covariates into sets of binary indicators
. labeledHeatmap now accepts arguments showRows and showCols that
allow one show a subset of the heatmap without having to explicitly
subset all row- and column-specific arguments
. branchSplitFromStabilityLabels.individualFraction can now work with
missing entries in cluster labels
. New function signifNumeric for rounding numeric columns of a data
frame.
. Bugfix in corFast: argument 'use' is now interpreted properly
(thanks to Thomas Mohr for the report).
. Argument networkType has been removed from the function
pickSoftThreshold.fromSimilarity where it has not been used; help
file has been adjusted accordingly (thanks to Max Moldovan for
reporting the issue).
. mtd.mapply now prints a more informative error message.
. bugfix in GOenrichmentAnalysis which now works again.
2018/03/21: 1.63-2
. TOM calculation now gives 0 for completely unconnected nodes,
instead of returning NaN
2018/02/26: 1.63
. Bugfix in blockwiseModules fixes a crash caused by supplying weights
to bicor
. DIFF: correlation options such as maxPOutliers are now by default
used throughout function blockwiseModules. New argument
useCorOptionsThroughout can be used to switch to old behaviour where
the arguments were used only for network construction.
2018/02/10: 1.62
. New functions sampledBlockwiseModules and
sampledHierarchicalConsensusModules carry out network analysis
repeatedly on resampled data.
. TOM calculations can optionally use internal matrix algebra rather
than R- (or system-)provided BLAS, controlled by argument
useInternalMatrixAlgebra.
. Pearson correlation (function cor) now accepts individual sample
weights for arguments x and y. When both weights are supplied (and
for correlation of a columns in a single matrix), the weights are a
product of the weights for the two vectors being correlated.
Denominators are calculated separately using separate weights, which
leads to slightly different results than standard weighted
correlation.
. Most network construction functions now also accept optional weights.
. hierarchicalConsensusModules can now optionally perform gene/module
pruning and merging iteratively.
. New functions pruneConsensusModules and
pruneAndMergeConsensusModules implement the pruning and iterative
pruning/merging of hierarchical consensus modules.
. Network construction functions now accept argument
suppressTOMForZeroAdjacencies whose effect is to set TOM to zero for
all node pairs with zero adjacency.
. Bugfix in individualTOMs: function now works with default
useDiskCache
. Module eigengenes returned by blockwiseConsensusModules now carry
names copied from names of multiExpr
. New function imputeByModule
. Bugfix in verboseBoxplot and verboseBarplot: the function now
honors the setting of addScatterplot and correctly interprets point
color and other arguments when they are vectors.
. Enhancements and bugfixes in TOMplot which should work with all
data sizes and dendrogram complexities.
. Function formatLabels now avoids over-splitting labels that already
contain a newline character.
. Function labeledHeatmap can plot row labels on the right, specified
via argument yLabPosition.
. Bugfix in internal function .networkCalculation
2017/08/04: 1.61
. Bugfix in consensusCalculation: function works with mean consensus.
. New arguments pch and plotPriority for verboseScatterplot.
. Function pmin has been removed since it incorrectly duplicates
base::pmin.
. Function GOenrichmentAnalysis is deprecated. Please use function
enrichmentAnalysis from R package anRichment, available from
https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/
2017/07/07: 1.60
. empiricalBayesLM expanded with additional arguments allowing
specification of initial fit function
. DIFF: New branch split function that works with stability labels,
branchSplitFromStabilityLabels.individualFraction, that tweaks the
branch dissimilarity measure to work better when one branch is large
and one small. To reproduce old results, use argument
stabilityCriterion = "Common fraction" to functions
hierarchicalConsensusModules and blockwiseConsensusModules.
. verboseBoxplot and verboseBarplot can now optionally overlay
scatterplots of the underlying data (thanks to Zhijin (Jean) Wu for
suggestion and code).
. Bugfix in enrichmentAnalysis: function does work when the number of
reported terms is zero. (Thanks to Zhijie Cao for bug report and
fix.)
. New functionality that allows a hierarchical calculation of
consensus modules, with multiple new functions.
. New arguments colorHeightBase, colorHeightMax control layout in
function plotDendroAndColors
. Arguments controlling the legend size in heatmaps with legends
been tweaked to make the legend width independent of the width of
the plotting region.
. The horizontal adjusting of row labels in labeledHeatmap can now be
set using the new argument x.adj.lab.y.
. Bugfix in mtd.susbet: function now works properly when invert is
TRUE.
. formatLabels can now format strings to a maximum width in user
coordinates and shorten the results to a given number of lines.
. Limitation to block sizes less than the integer addressing limit
(sqrt(2^31)) has been removed.
. Multiple mtd.... functions now return NULL when the input multiData
argument has length zero.
. Function adjacency now accepts corOptions in both character and list
formats.
. New function minWhichMin that calculates the row- or column-wise
minimum and index of the minimum.
. New functions pmin.fromList, pmean.fromList, pquantile.fromList, for
parallel minimum, mean and quantile whose input is a list of
identically sized arrays; functions pmin, pmean and pquantile now
use compiled code and should be substantially faster and more memory
efficient.
. Bugfix in function blockwiseModules: corrected conditional module
removal if too few genes remain.
. pickSoftThreshold is now faster thanks to Alexey Sergushichev; new
argument gcInterval allows the user to fine tune frequency of garbage
collection to suit the size of the data.
. verboseBarplot now takes argument ylim which defaults to
incorporating all bar heights plus error bars (if requested)
. Cleanup in function labeledHeatmap: incorrect text and color label
offsets and widths fixed. The corresponding arguments xColorWidth,
yColorWidth are now measured in user units rather than fractions of
overall width and height.
. New functions bicovWeightFactors and bicovWeightsFromFactors
2016/05/30: 1.52
. New function plotMultiHist for plotting multiple histograms in one
plot
. New functions multiGrep, multiGrepl, multiSub, multiGSub
. New argument invert in mtd.subset allows consistent excluding of
rows and columns from multiData structures.
. Bugfix in modulePreservation: accuracy statistics now work also with
a single module. Thanks to Victor Hanson-Smith for pointing this
out.
. mtd.rbindSelf now warns when colnames of the individual data sets do
not agree.
2016/03/08: 1.51
. DIFF: Defaults for the number of pre-clustering centers in
blockwise[Consensus]Modules, projectiveKMeans and
consensusProjectiveKMeans have changed to prevent the
pre-clustering from becoming too long. To reproduce old results, use
(nPreclusteringCenters or nCenters) = min(nGenes/20,
maxBlockSize^2/nGenes), where nGenes is the number of genes (variables)
in the input data.
2016/02/23: 1.50
. Bugfix in function cor: function now correctly handles cases where
columns have missing data placed such that the remaining entries
(after removing missing values) have zero variance. Thanks to Pasha
Mazin for pointing this out.
. New function consensusRepresentatives for selecting consensus representatives
from multi-data.
. Cleanup in plotOrderedColors should results in better placement of
'rowText' under blocks of colors.
. Minor change in spacing for row text in plotOrderedColors that also affects
plotColorUnderTree and plotDendroAndColors
. TOM calculation functins (TOMsimilarity, blockwiseIndividualTOMs,
blockwiseModules) now accept argument replaceMissingAdjacencies that
allows the underlying code to replace missing adjacencies with an
appropriate value for zero-strength link.
. moduleEigengenes is now more resistant to problems with missing data
and zero-variance variables.
2015/12/27: 1.49
. DIFF: goodGenes, goodGenesMS, goodSamplesGenes, goodSamplesGenesMS get an
argument `tol' to compare the variance against, rather than against
zero. This prevents erroneous retaining of zero-variacen genes
because of numeric under/overflow errors in the fast calculation of
variance. This may possibly result in removal of genes that were
retained in WGCNA versions 1.47-2 and newer, but should remove the
same genes as 1.47-1 and older.
2015/12/16: 1.48-2
. Bugfix in our local copy of heatmap, called from TOMplot, based on
the bug report
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=16583 . Thanks to
Duncan Murdoch for pointing it out
. Function goodSamplesGenesMS can now work with data frames within the
multiExpr structure, rather than just matrices.
2015/11/03: 1.48-1
. TOMplot now uses my own dendrogram drawing routine which should not
run into the stack/memory allocation problems of the standard
plot.dendrogram function.
2015/10/29: 1.48
. Bugfix in pickHardThreshold (and pickHardThreshold.fromSimilarity):
when the input is a similarity matrix rather than expression data,
the function no longer crashes.
2015/10/09: 1.47-6
. Bug in consensusTOM fixed that caused a spurious error
"File names to save blocks of consensus TOM are not unique."
when calculating with more than on block.
. DIFF: Function consensusProjectiveKMeans can (and will by default) impute
missing data. This may cause differences in preclustering when
missing data are present. To reproduce old results, use
argument imputeMissing = FALSE.
2015/09/30: 1.47-5
. Function consensusKME is now using internal code for re-arranging
rather than relying on reshape's melt-cast combination due to
performance issues with larger data sets.
. Imports from/dependence on reshape have been dropped.
. blockwiseConsensusModules accepts argument cacheBase which replaces
the default "." that has been used.
. labelPoints now returns a data frame with the label positions, and
accepts argument doPlot that optionally turns off the plotting of
the labels.
. bicor now produces a better-worded warnings about zero or missing
MAD.
2015/08/07: 1.47-4
. DIFF: projectiveKMeans now by default imputes missing data in
datExpr at the start of the function.
This can lead to somewhat different output; old
behaviour can be forced by setting imputeMissing = FALSE. This
change does not affect blockwiseModules since blockwiseModules
imputed missing data before calling projectiveKMeans.
. Internal code cleanup: several ifelse calls changed to if else
constructs to avoid issues with ifelse generics defined by
bioconductor
. pickHardThreshold is now more resistant to genes (columns) that have
zero variance. However, their connectivity is considered 0.
. DIFF: Bugfix in internal code fixes an error in blockwiseModules and
blockwiseConsensusModules where blocks determined by pre-clustering
were incorrectly merged. In rare cases this may cause differences to previous
results. Thanks to Elmar Tobi for reporting this.
2015/06/27: 1.47-2
. goodGenes and goodSamples, along with their MS versions, should now
run faster thanks to a code clean-up
2015/06/18: 1.47-1
. Bugfix in empiricalBayesLM fixes a crash in the function.
2015/06/13: 1.47
. Functions plotCor, plotMat and rgcolors.func from sma have been re-introduced
. empiricalBayesLM is now more robust to missing values, particularly
when OLS regression fails due to missing values making some of the
covariates constant.
. Bugfix in bicovWeights fixes crash when there is one variable with
MAD = 0.
. Function blockwiseModules can now optionally use module merging
criteria derived from stability studies.
. Functions blockwiseModules, blockwiseIndividualTOMs and
consensusBlockwiseModules now accept argument blockSizePenaltyPower
that lets the user specify the severity of penalty for blocks
exceeding maximum size.
. Functions projectiveKMeans and consensusProjectiveKMeans now accept
Inf for sizePenaltyPower.
. Function labeledHeatmap.multiPage now accepts more explicit
arguments (rather than relying on ... as before)
and correctly handles separator lines.
2015/03/28: 1.46
. Functions inherited from the now-defunct package sma have been
removed.
2015/03/27: 1.45
. New function empiricalBayesLM for removing unwanted variation due to
given covariates from high-dimensional data
. New function bicovWeights for assigning weights to observations
based on whether they are suspected outliers
. labeledHeatmap and friends now accept argument keepLegendSpace
. labeledHeatmap now returns information about positions of individual
boxes in the heatmap.
. labeledHeatmap now accepts argumens xColorOffset and yColorOffset
controling the gap between color labels and the heatmap itself.
2015/02/06: 1.43-11
. Bugfix in C code fixes memory allocation errors with large data
sets. The C code was also made more consistent in the use of
size_t whenever needed and possible.
. Bugfix in labeledHeatmap fixes the direction of extended separator
lines for x-axis labels with angle other than the default 45
degrees.
2015/01/23: 1.43-10
. Bugfix in function blockwiseIndividualTOMs and functions that use it
(blockwiseConsensusModules, consensusTOM) fixes a bug that caused
crashes when more than one blocks were used.
2015/01/15: 1.43
. Package now imports AnnotationDbi and GO.db
. Function blueWhiteRed gains argument endSaturation that allows the
user to lighten the colors at the end of the range, at the expense of
saturation.
. Function labeledHeatmap gains additional arguments allowing the user
to place horizontal and vertical divider lines into the heatmap.
. Bugs introduced into GOenrichmentAnalysis in the previous release
are now fixed.
2014/11/25: 1.42
. Function TrueTrait has been re-worked and the argument Strata to it
is no longer accepted.
. labeledHeatmap.multiPage now works with 1-column or 1-row matrices.
. The textMatrix argument to labeledHeatmap and
labeledHeatmap.multiPage is now allowed to be a (dimensionless)
vector as long as its length is consistent with the dimensions of
the input Matrix.
. Bugfix in function formatLabels fixes sometimes incorrect start of
formatted labels.
. Bugfixes in function TrueTrait
. DIFF: Bugfix in mtd.branchEigengeneDissim that primarilly affects
blockwiseConsensusModules. The consensus quantile was incorrectly
applied, which led to overly aggressive module merging. The bugfix
will lead to a different final modules if useBranchEigengeneDissim
was TRUE. To reproduce old behavior, use argument
reproduceBranchEigennodeQuantileError = TRUE.
. New function consensusTOM implements calculation of consensus TOM
in a stand-alone function; this calculation was previously hidden
inside blockwiseConsensusModules.
. Network calibration methods in consensusTOM now include full
quantile normalization
. DIFF: bugfix in blockwiseIndividualTOMs that affects
blockwiseIndividualTOMs as well as blockwiseConsensusModules: The
soft-thresholding power for set 1 was used for all sets. This bug
has bow been fixed; to reproduce old calculations, change the old
code to use the same power for all sets. I apologize for this rather
serious omission.
. blockwiseIndividualTOMs gains additional output components.
. Internal C code changed some index variables from int to size_t.
. Function individualTOMs now uses a more memory-efficient way to call
the internal compiled code.
. Bugfix in mtd.apply fixes occasional spurious crashes
. Function mtd.apply now copies the 'names' attribute from input to
the output
. Function mtd.subset can now subset columns based on column names,
not just numeric indices.
. Function votingLinearPredictor can now tolerate missing data in the
predictor variables (features).
. blockwiseModules gains a new argument loadTOM.
2014/06/13: 1.41-1
. DUP = FALSE removed from all .C calls since the argument is
deprecated. This means that memory requirements may increase in some
situations.
2014/06/12: 1.41
. New function shortenStrings
. Changed several packages we depend on from Depends: to Imports:
. New functions prependZeros and formatLabels
. Bugfix in userListEnrichment: function no longer crashes when there
are no "significant" overlaps
. New function intramodularConnectivity.fromExpr
2014/05/07: 1.40
. Functions blockwise[Consensus]Modules and
recut[Blockwise,Consensus]Trees get new arguments minSplitHeight and
minAbsSplitHeight that get passed to cutreeDynamic.
. Arguments for blockwiseModules have been re-ordered to group them
and make it easier to find the right setting.
2014/04/28: 1.39
. Function exportNetworkToVisANT can now restrict connections to a
given number of top connections.
. Function exportNetworkToVisANT returns the resulting data frame
invisibly.
. Function modulePreservation gains the ability to run the
calculations in parallel, controlled by argument
'parallelCalculation'.
. Function modulePreservation gains the ability to explicitly specify
test sets for each reference network, via parameter testNetworks.
. Functions matchLabels and overlapTable have been expanded with new
functionality and arguments. matchLabels now works with any labels
(not just numeric or color labels) and can handle missing labels by
removing them.
. Bug in function multiData2list fixed: function now returns a simpler
(and correct) list.
. Crash-causing bug in mtd.rbindSelf fixed.
2014/01/08: 1.37
. New functions multiUnion and multiIntersect
. New function labeledHeatmap.multiPage produces labeled heatmaps
divided into multiple plots (pages).
. plotColorUnderTree and plotOrderedColorsnow produce more precise
"center" and "right" text alignment.
. Maximum block size in blockwiseModules, blockwiseConsensusModules
and blockwiseIndividualTOMs (argument 'maxBlockSize') is now limited
to be less than sqrt(2^31) to prevent problems with C and Fortran
routines. The same limitation also applies to the 'preferredSize'
argument of projectiveKMeans and consensusProjectiveKMeans.
. Occasional bug when saving and loading permutation test results in
modulePreservation fixed.
2013/11/22: 1.36
. Needs dynamicTreeCut 1.61 or higher.
. Bugfix in mtd.mapply fixes a crash.
. Warning message in mtd.subset cleaned up.
. New function multiData to conveniently create multiData structures.
. The color palette of blueWhiteRed has been tweaked to provide
lighter extreme colors which makes it easier to read black text
superimposed on the strongest colors.
. More descriptive error message in cor() and bicor() when input
contains missing data and 'use = "all.observations"'.
2013/11/04: 1.35
. Function accuracyMeasures now works also with factors.
. Function moduleEigengenes calls impute.knn only if there are any
missing data.
. Functions mtd.apply, mtd.applyToSubset, and mtd.mapply gain
arguments controling whether and how progress should be displayed;
they also gain arguments that let the user specify calculation on
only a subset of the input sets.
2013/10/10: 1.34
. Function verboseBarplot gains argument addCellCounts that enables
display of counts above each bar.
. Function mtd.subset gains the argument 'permissive' that allows
subsetting of "loose" multiData structures as well as 'drop' that
controls dropping of dimensions with extent 1.
. Internal: Depends and Imports fields were cleaned up as per new CRAN
requirements. Users should be aware that loading and attaching WGCNA
now does not automatically attach all packages from which WGCNA imports.
. Potentially serious bug has been fixed in the internal C code for
calculations of correlation (function cor()). This bug seems to have led to
correlation sometimes returning 0 where it should have returned an NA.
2013/08/29: 1.33
. mtd.apply and mda.applyToSubset gain argument mdaCopyNonData that controls whether
non-data components of input should be copied to output
. Bug in matchLabels fixed that led to non-integer color labels if two
reference modules had the same size.
. New function plotOrderedColors that extends plotColorUnderTree to