forked from lgatto/pRoloc
-
Notifications
You must be signed in to change notification settings - Fork 0
/
NEWS
1200 lines (856 loc) · 34.6 KB
/
NEWS
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
Changes in version 1.23.2
-------------------------
- Add mcmc helper functions.
- New logPosteriors accessor for MAPParams object.
- New plotConsProfiles function, contributed by Tom Smith (see PR
#131).
- Update TAGM vignette, refering to workflow <2019-03-14 Thu>
Changes in version 1.23.1
-------------------------
- Add note about missing data in QSep man <2018-10-31 Wed>
- Add mcmc-helper documentation <2018-11-04 Sun>
- Fixing numerical instability in Cholesky decomposition (see #124)
<2018-11-30 Fri>
- Add option to display or not display grid in plot2D <2018-12-12 Wed>
- `mrkHClust` now uses `mrkConsProfiles` and returns the `hclust`
object - see issue #130 for details and background <2018-12-19 Wed>
Changes in version 1.23.0
-------------------------
- New version for Bioc 3.9 devel
Changes in version 1.22.0
-------------------------
- New version for Bioc 3.8 release
Changes in version 1.21.9
-------------------------
- Fix type in vignette header <2018-09-18 Tue>
- Fix bug in plot method for ThetaRegRes object <2018-09-24 Mon>
Changes in version 1.21.8
-------------------------
- Add an `fcol` argument to `plotDist` to plot and colour all profiles
<2018-08-09 Thu>
Changes in version 1.21.7
-------------------------
- Use BiocManager in vignette
- Fix bug in plot2D: pass ... to hexbin <2018-08-02 Thu>
Changes in version 1.21.6
-------------------------
- Use BiocManager in installation instructions
Changes in version 1.21.5
-------------------------
- Added new section in Bayesian spatial proteomics vignette detailing
mcmc output processing <2018-07-07 Sat>
Changes in version 1.21.4
-------------------------
- Fix bugs in tagmMcmcPredict, where fcol was ignored <2018-06-05 Tue>
- Order vignettes by prefixing the files with numbers <2018-06-05 Tue>
Changes in version 1.21.3
-------------------------
- New TAGM-MCMC generative model, contributed by Oliver Crook
<2018-05-18 Fri>
Changes in version 1.21.2
-------------------------
- Version bump for BiocStyle update: Vignette needed to be rebuilt to
have bug fixed in BiocStyle footnote rendering.
Changes in version 1.21.1
-------------------------
- Fix bug in higlightOnPlot with missing fcol (see #105)
<2018-05-03 Thu>
- New TAGM-MAP generative model, contributed by Oliver Crook
<2018-05-18 Fri>
- New `plotEllipse` function to visualise and assess TAGM models
<2018-05-18 Fri>
Changes in version 1.20.0
-------------------------
- New Bioconductor release 3.7
Changes in version 1.19.4
-------------------------
- Fix regression bug in knntl function <2018-04-12 Thu>
Changes in version 1.19.3
-------------------------
- Use `dplyr::left_join` without attaching `dplyr` to avoid collision
between `Biobase::exprs` and `dplyr::exprs` <2018-04-04 Wed>.
- Typo in warning to install rgl <2018-03-27 Tue>
Changes in version 1.19.2
-------------------------
- Fix bug in QSep that prevented to set non-default fcol
<2018-01-29 Mon>
Changes in version 1.19.1
-------------------------
- Fix bug in private dimred and set appropriate number of colnames
<2017-11-07 Tue>
- New `nipals` method in dimensionality reduction for plot2D (closes
issue #103) <2018-01-16 Tue>
Changes in version 1.19.0
-------------------------
- Bioconductor devel 3.7
Changes in version 1.18.0
-------------------------
- Bioconductor release 3.6
Changes in version 1.17.5
-------------------------
- Filtering for unique features when running plot2D with t-SNE method
<2017-10-15 Sun>
Changes in version 1.17.4
-------------------------
- Added new (private) dimred function that computes dimensionality
reduction <2017-06-05 Mon>
- Add F1000research workflow to citations <2017-06-22 Thu>
- Classification functions now return the classification score matrix
for all classes as a single column in fData, rather that each class
as its own fData column. <2017-09-01 Fri>
Changes in version 1.17.3
-------------------------
- Convert vignettes to Rmd with html output <2017-05-25 Thu>
- Import, rather than suggest Rtsne <2017-05-25 Thu>
Changes in version 1.17.2
-------------------------
- phenoDisco speed improvements and added support for t-SNE
<2017-05-19 Fri>
Changes in version 1.17.1
-------------------------
- Support Rtsne's new pca_center and pca_scale arguments
<2017-05-02 Tue>
Changes in version 1.17.0
-------------------------
- Version bump for Bioc devel 3.6
Changes in version 1.16.0
-------------------------
- Version bump for Bioc release 3.5
Changes in version 1.15.9
-------------------------
- update biomart attribute names to relect changes <2017-04-20 Thu>
Changes in version 1.15.8
-------------------------
- New mrkConsProfiles function to calculate average/consensus marker
profiles <2017-04-11 Tue>
Changes in version 1.15.7
-------------------------
- Fix warnings and notes <2017-02-25 Sat>
- Add section about dimensionality methods reduction and t-SNE in the
tutorial <2017-03-07 Tue>
- Fix error due to new uniprot attribute names <2017-04-06 Thu>
Changes in version 1.15.6
-------------------------
- fix (unexported) remap function - see issue #92 <2016-12-15 Thu>
- plot2Ds now only adds segments when the featureNames are identical
<2017-01-11 Wed>
- Import (rather than Suggest) hexbin <2017-01-18 Wed>
- Increase margin in QSep plotting (contributed by S. Gibb)
<2017-02-07 Tue>
Changes in version 1.15.5
-------------------------
- Update plotDist to use sampleNames() to label x axis ticks and
getUnknowncol() as default pcol (see issue #91) <2016-11-08 Tue>
- xlab and ylab are args in plotDist <2016-12-04 Sun>
Changes in version 1.15.4
-------------------------
- Update human markers - see pRolocdata's issue 21
https://github.com/lgatto/pRolocdata/issues/21 <2016-11-08 Tue>
Changes in version 1.15.3
-------------------------
- Fix bug in plot2D to ignore fcol when using hexbin method
<2016-11-04 Fri>
Changes in version 1.15.2
-------------------------
- Fix Arabidopsis parameters for biomaRt questions: 'TAIR locus ID'
is now 'Stable gene ID'. Changed in several manual files and
dunkley2006params. <2016-11-02 Wed>
Changes in version 1.15.1
-------------------------
- new plot3D function <2016-10-27 Thu>
- update CITATION <2016-10-27 Thu>
- use predict:::predict.plsa, as it is not exported anymore
<2016-11-01 Tue>
Changes in version 1.13.16
--------------------------
- removing visualTest from suggest, as plotting tests currently
disabled (see https://github.com/MangoTheCat/visualTest/issues/19 for
details) <2016-10-07 Fri>
Changes in version 1.13.15
--------------------------
- Fix bug in plot,QSep with NAs <2016-09-09 Fri>
- Adapt tl vignette to new hpar <2016-09-15 Thu>
Changes in version 1.13.14
--------------------------
- Pass ... in levelPlot,QSep <2016-09-06 Tue>
- Various improvements to the tutorial vignette <2016-09-07 Wed>
- Fix bug in QSep to honour fcol <2016-09-09 Fri>
Changes in version 1.13.13
--------------------------
- Added plot3D, equivalent to plot2D, but using rgl in 3 dimensions
<2016-09-03 Sat>
- Parametrise logging in knntlOptimisation to reduce object size
<2016-09-06 Tue>
- New mrkHClust function to plot a dendrogram of subcellular markers
<2016-09-06 Tue>
Changes in version 1.13.12
--------------------------
- Remove verbose argument from getMarkerClasses function
<2016-08-23 Tue>
- plot2D has new addLegend argument <2016-08-23 Tue>
- addLegend default position is now bottomleft (requested by Lisa)
<2016-08-23 Tue>
- new hexbin plot2D method <2016-08-28 Sun>
Changes in version 1.13.11
--------------------------
- Add a norm agument to QSep's plotting functions to visualise
normalised and raw distances <2016-08-22 Mon>
- New zeroInBinMSnSet function to visualise rowSums <2016-08-23 Tue>
Changes in version 1.13.10
--------------------------
- Send biomart queries in getGOFromFeatues in chunks - see issue #85
for details <2016-08-20 Sat>
Changes in version 1.13.9
-------------------------
- new QSep infrastructure to assess spatial resolution
<2016-08-17 Wed>
- Use %age of total variance in plot2D's scree plot <2016-08-17 Wed>
- fixed bug in combineThetaRegRes <2016-08-19 Fri>
Changes in version 1.13.8
-------------------------
- fDataToUnknown accepts from = NA <2016-08-10 Wed>
Changes in version 1.13.7
-------------------------
- Added an lda method to plot2D <2016-08-08 Mon>
Changes in version 1.13.6
-------------------------
- Fixed bug in addGoAnnotations <2016-07-29 Fri>
Changes in version 1.13.5
-------------------------
- Fixed bug in show method for ThetaRegRes <2016-06-08 Wed>
- Profiled knntl code so it's now much faster. Added more unit tests
for knntl <2016-06-10 Fri>
- Fixed bug in plotDist x-axis labelling <2016-06-14 Tue>
Changes in version 1.13.4
-------------------------
- Updated mouse pRolocmarkers <2016-06-02 Thu>
Changes in version 1.13.3
-------------------------
- Fix bug in mirrorX/Y highlightOnPlot - see problem 1 in issue #79 <2016-05-31 Tue>
Changes in version 1.13.2
-------------------------
- Version bump to trigger package rebuilding now that purl()'ing
issue has been correctly identified. knitr does not create
purl()'ed (Stangle equivalent) .R files if _R_CHECK_TIMINGS_ is
set, which the build system was setting. Now it's not set, so these
.R files are now created. See
https://github.com/yihui/knitr/issues/1212 for more. d.tenenbaum
Changes in version 1.13.1
-------------------------
- Added keepNA argument to goTermToId so that if a GO term becomes
obsolete and you cannot replace it with the ID name, you have
the option to either replace it with a NA (previous and current
default option) or now with keepNA = FALSE the term name will be
replaced with the id name <2016-05-25 Wed>
- Bump version of all packages that use knitr for vignettes. This is
because of an issue (now fixed) in knitr which failed to create
purl()'ed R files from vignette sources and include them in the
package. This version bump will cause these packages to propagate
with those R files included. d.tenenbaum
Changes in version 1.13.0
-------------------------
- Version bump for new Bioc devel
Changes in version 1.12.0
-------------------------
- Version bump for Bioc release version 3.3
Changes in version 1.11.23
--------------------------
- New gomarkers functionality for adding annotation information
to spatial proteomics data and accompanying new vignette
<2016-04-18 Mon>
- Added unit tests <2016-04-20 Wed> <2016-04-21 Thu>
- Moved makeNaData[2] and whichNA to MSnbase <2016-04-21 Thu>
- Renamed addGoMarkers and orderGoMarkers to addGoAnnotations
and orderGoAnnotations and all associated documentation.
Vignette also renamed to pRoloc-goannotations
<2016-04-21 Thu>
Changes in version 1.11.22
--------------------------
- fix bug in knntlOptimisation to allow passing of th matrix
with 1 column <2016-04-08 Fri>
Changes in version 1.11.21
--------------------------
- fix bug in getParams method = 'max' <2016-04-07 Thu>
Changes in version 1.11.20
--------------------------
- Update plotDist signature to support different types and pch
<2016-04-05 Tue>
Changes in version 1.11.19
--------------------------
- Update dunkley2006params <2016-04-01 Fri>
Changes in version 1.11.18
--------------------------
- Update dunkley2006params <2016-03-30 Wed>
Changes in version 1.11.17
--------------------------
- Selective imports <2016-03-20 Sun>
Changes in version 1.11.19
--------------------------
- Update dunkley2006params <2016-04-01 Fri>
Changes in version 1.11.18
--------------------------
- Update dunkley2006params <2016-03-30 Wed>
Changes in version 1.11.17
--------------------------
- Selective imports <2016-03-20 Sun>
Changes in version 1.11.16
--------------------------
- Update package startup msg <2016-03-11 Fri>
Changes in version 1.11.15
--------------------------
- Clarify that score during optim are not a reflection of final
assignment accuracy <2016-03-01 Tue>
Changes in version 1.11.14
--------------------------
- fix build error due to doi/url confusion <2016-03-01 Tue>
Changes in version 1.11.13
--------------------------
- new method argument added to knntlOptimisation that allows
optimisation of class weights as per Wu and Dietterich's
original k-NN TL method <2016-02-19 Fri>
- seed argument added to knntlOptimisation for reproducibility
<2016-02-22 Mon>
- New section in tl vignette describing preparation of auxiliary PPI
data <2016-02-29 Mon>
Changes in version 1.11.12
--------------------------
- the colour and pch setters now invisibly return the old values
<2016-02-17 Wed>
Changes in version 1.11.11
--------------------------
- added error message when sampleNames differ between datasets
in an MSnSetList when using remap function <2016-02-11 Thu>
Changes in version 1.11.10
--------------------------
- Update colours man page to document change in default colour
palette <2016-02-08 Mon>
Changes in version 1.11.9
-------------------------
- Lisa's colour palette is now default. Old colours can be accessed
and set with get/setOldcol <2016-02-04 Thu>
Changes in version 1.11.8
-------------------------
- New Lisa cols and changed default unknown col <2016-02-03 Wed>
- mrkVecToMat has been updated so that the column order reflects
the factor levels of fcol, rather than calling unique on fcol.
This change means that the order of the classes in fcol are
now consistent between plot2D and new visualisation apps that
rely on mrkVecToMat. <2016-02-03 Wed>
Changes in version 1.11.7
-------------------------
- Various non-visible changes. <2016-01-19 Tue>
Changes in version 1.11.6
-------------------------
- new classWeights function <2015-12-26 Sat>
Changes in version 1.11.5
-------------------------
- highlightOnPlot support labels = TRUE to use featureNames as labels
<2015-12-21 Mon>
- selective ggplot2 import <2015-12-21 Mon>
- highlightOnPlot also support a vector of feature names in addition
to an instance of class FeaturesOfInterest <2015-12-21 Mon>
Changes in version 1.11.4
-------------------------
- plot2D: Mirror PCs even when not plotting, addressing issue #68
<2015-12-18 Fri>
Changes in version 1.11.3
-------------------------
- Update dunkley2006params to use plant_mart_30 <2015-12-16 Wed>
- API change in plot2D: to plot data as is, i.e. without any
transformation, method can be set to "none" (as opposed to passing
pre-computed values to method as in previous versions). If object
is an MSnSet, the untransformed values in the assay data will be
plotted. If object is a matrix with coordinates, then a matching
MSnSet must be passed to methargs. <2015-12-16 Wed>
Changes in version 1.11.2
-------------------------
- Internally using MartInterface to query individual mart servers to
bypass the biomart.org downtime <2015-12-09 Wed>
Changes in version 1.11.1
-------------------------
- New orgQuants function and update to getPredictions
<2015-10-13 Tue>
- Deprecate minClassScore replaced by getPredictions
<2015-10-19 Mon>
- Add pRolocVisMethods and check for new apps in
pRolocGUI <2015-10-19 Mon>
- new fDataToUnknown function <2015-10-23 Fri>
- New section in vignette describing readMSnSet2 <2015-11-30 Mon>
Changes in version 1.11.0
-------------------------
- Bioc devel version 3.3
Changes in version 1.10.0
-------------------------
- Bioc release version 3.2
Changes in version 1.9.7
------------------------
- New SpatProtVis visualisation class <2015-08-13 Thu>
- add link to explanation of supportive/uncertain reliability scores
in tl vignette <2015-09-02 Wed>
Changes in version 1.9.6
------------------------
- Update REAMDE with TL ref
- Update refs in lopims documentation <2015-07-30 Thu>
Changes in version 1.9.5
------------------------
- update doc <2015-07-15 Wed>
Changes in version 1.9.4
------------------------
- Add reference to TL paper and link to lpSVM code <2015-07-06 Mon>
- highlightOnPlot throws a warning and invisibly returns NULL instead
of an error when no features are in the object <2015-07-08 Wed>
- highlightOnPlot has a new labels argument <2015-07-10 Fri>
Changes in version 1.9.3
------------------------
- Clarify error when no annotation params are provided
<2015-05-11 Mon>
- support for matrix-encoded markers <2015-05-19 Tue>
- New default in addLegend: bty = "n" <2015-05-20 Wed>
- getMarkers now supports matrix markers <2015-05-20 Wed>
- getMarkerClasses now supports matrix markers <2015-05-20 Wed>
- markerMSnSet and unknownMSnSet now support matrix markers
<2015-05-20 Wed>
- sampleMSnSet now supports matrix markers <2015-05-23 Sat>
- updated yeast markers and added uniprot ids <2015-05-27 Wed>
- plot2D support a pre-calculated dim-reduced data matrix as method
parameter to avoid recalculation <2015-05-27 Wed>
Changes in version 1.9.2
------------------------
- Lisa's colour palette <2015-05-08 Fri>
Changes in version 1.9.1
------------------------
- new plot2Ds function to overlay two data sets on the same PCA plot
[2015-04-17 Fri]
- regenerate biomart data used by setAnnotationParams
[2015-04-24 Fri]
- new setStockcolGui function to set the default colours manually via
a simple interface [2015-04-29 Wed]
- new move2Ds function to produce an transition movie between two
MSnSets [2015-04-29 Wed]
- functions to convert GO ids to/from terms. See ?goTermToId for
details <2015-05-08 Fri>
Changes in version 1.9.0
------------------------
- new devel version for Bioc 3.2
Changes in version 1.7.13
-------------------------
- use donttest instead of dontrun [2015-04-09 Thu]
Changes in version 1.7.12
-------------------------
- don't run knntl example to reduce checking time and timeout on
Windows [2015-04-08 Wed]
Changes in version 1.7.11
-------------------------
- fix splitTh, closes issue #49 [2015-04-06 Mon]
Changes in version 1.7.10
-------------------------
- Change in vignette to work on zin1: using 12 random th rows. See
issue #49 for details. Fixed in version 1.7.11. [2015-04-03 Fri]
Changes in version 1.7.9
------------------------
- updated tl vignette [2015-04-02 Thu]
- depending on latest (1.5.8) pRolocdata [2015-04-02 Thu]
Changes in version 1.7.8
------------------------
- updating tl vig [2015-04-02 Thu]
- update getParams documentation [2015-04-02 Thu]
Changes in version 1.7.7
------------------------
- renaming theta.scores to knntl.scores [2015-03-24 Tue]
Changes in version 1.7.6
------------------------
- added the theta inductive transfer infrastructure [2015-02-05 Thu]
- theta vignette stub [2015-02-06 Fri]
- rename getClasses to getMarkerClasses [2015-02-06 Fri]
- added the infrastructure to create GO MSnSet [2015-02-07 Sat]
- Fixed ml vignette [2015-02-16 Mon]
- new filterZeroRows function [2015-03-10 Tue]
- hpa data section [2015-03-10 Tue]
- theta sections [2015-03-10 Tue]
- deprecate getRegulari[z|s]edParams [2015-03-11 Wed]
Changes in version 1.7.5
------------------------
- Fix vignettes: run bibtex and pdflatex twice and typo
[2015-02-03 Tue]
Changes in version 1.7.4
------------------------
- Use default Sweave call to build vignette [2015-01-24 Sat]
Changes in version 1.7.3
------------------------
- use Biocstyle [2015-01-23 Fri]
- replace library/require by requireNamespace [2015-01-23 Fri]
Changes in version 1.7.2
------------------------
- added t-SNE method to plot2D [2015-01-14 Wed]
- Updated NAMESPACE imports [2015-01-14 Wed]
Changes in version 1.7.1
------------------------
- updated vignettes with markers.orig [2014-10-30 Thu]
- updated ml tests [2014-10-30 Thu]
Changes in version 1.7.0
------------------------
- new devel version, Bioc 3.1
Changes in version 1.6.0
------------------------
- new stable version, Bioc 3.0
Changes in version 1.5.19
-------------------------
- added Video tag in DESCRIPTION [2014-10-07 Tue]
Changes in version 1.5.18
-------------------------
- HUPO 2014 poster [2014-01-02 Thu]
Changes in version 1.5.17
-------------------------
- fix 'replacing previous import by MLInterfaces::plot when loading
pRoloc' warning by using specific importFrom [2014-09-27 Sat]
Changes in version 1.5.16
-------------------------
- new pRolocGUI section [2014-08-15 Fri]
- new foi section [2014-08-16 Sat]
Changes in version 1.5.15
-------------------------
- svmOpt sigma defaults changed from 10^(-2:3) to 10^(-3:2)
[2014-08-15 Fri]
- in xxxOptimisation, the best parameter(s) for the validation
classification runs are now chosen at random instead of using the
first best param (see change in pRoloc:::getBestParam that got a
sample argument defaulted to TRUE) [2014-08-15 Fri]
- When calculating macroF1 scores (xval and validation), NAs are set
to 0 (via MLInterfaces:::.macroF1(..., naAs0 = TRUE)). The macro F1
will not be NA (when mean of F1s is calculated) but lowered. This
avoids having an NA macro F1 when 1 (or more) classe(s) end(s) up
with NA (also set to 0) precision(s) or recall(s) [2014-08-15 Fri]
Changes in version 1.5.14
-------------------------
- add title to plotDist figures [2014-08-13 Wed]
Changes in version 1.5.13
-------------------------
- none
Changes in version 1.5.12
-------------------------
- support mirrorX/mirrorY in highlightOnPlot [2014-07-22 Tue]
Changes in version 1.5.11
-------------------------
- Remove plot2D outliers param [2014-07-10 Thu]
- fix subsetAsDataFrame for keepColNames and write unit test
[2014-07-11 Fri]
Changes in version 1.5.10
-------------------------
- alias lopims4 function [2014-07-01 Tue]
Changes in version 1.5.9
------------------------
- Export single steps of lopims [2014-06-23 Mon]
- Rephrase classifier parameter optimisation proceudres [2014-06-23 Mon]
Changes in version 1.5.8
------------------------
- nndistx_matrix function added to allow use of query matrix
when calculating knn distances [2014-06-18 Wed]
- nndist[x]_[matrix|msnset] are now available using the experted
nndist method [2014-06-18 Wed]
- markerSet and unknownSet renamed to markerMSnSet and unknownMSnSet
[2014-06-19 Thu]
- functions sampleMSnSet and testMSnSet added [2014-06-19 Thu]
- fix keepColNames in pRoloc:::subsetAsDataFrame - fcol was
always renamed to "markers" [2014-06-19 Thu]
Changes in version 1.5.7
------------------------
- add recommended biocView [2014-06-05 Thu]
Changes in version 1.5.6
------------------------
- addMarkers has a new mcol argument to set the markers feature
variable label [2014-05-29 Thu]
Changes in version 1.5.5
------------------------
- replaced MSVBAR::rmultnorm with mvtnorm::rmvnorm since the former
has been removed from CRAN and don't import [2014-05-21 Wed]
- Bug tracking [2014-05-26 Mon]
Changes in version 1.5.4
------------------------
- testMarkers gets an error argument [2014-05-14 Wed]
- plotDist now has a ylim argument [2014-05-21 Wed]
Changes in version 1.5.3
------------------------
- import all MLInterfaces [2014-04-30 Wed]
- new param optim secion in ml vignette [2014-05-05 Mon]
- various ml typos and pRolocmakers man update [2014-05-06 Tue]
Changes in version 1.5.2
------------------------
- In plotDist, ... is now passed to matlines instead of plot and has
a new lty parameter [2014-04-17 Thu]
- new highlightOnPlot function, using the new features of interest
infrastructure [2014-04-29 Tue]
Changes in version 1.5.1
------------------------
- new dunkley2006 pdunit object created with mclust 4.3
[2014-04-08 Tue]
- addMarker also accepts fcol and addMarkers unit test
[2014-04-14 Mon]
Changes in version 1.5.0
------------------------
- Bioc devel 3.0
Changes in version 1.4.0
------------------------
- Bioc release 2.14
Changes in version 1.3.19
-------------------------
- fixed error introduced with mclust 4.3 (that now returns the data
in the Mclust output - see comment in pRoloc:::gmmOutliers for
details) [2014-04-07 Mon]
Changes in version 1.3.18
-------------------------
- getPredictions can take class-specific scores [2014-04-04 Fri]
Changes in version 1.3.17
-------------------------
- fixed newly introduced bug (see 1.3.16) in
pRoloc:::subsetAsDataFrame - thank you unit tests for saving me,
again [2014-03-26 Wed]
Changes in version 1.3.16
-------------------------
- pRoloc:::subsetAsDataFrame now preserved original sample/column
names [2014-03-24 Mon]
- fixed wrong message when using col and pch in plot2D
[2014-03-25 Tue]
Changes in version 1.3.15
-------------------------
- updated pRolocmarkers("mmus") [2014-03-21 Fri]
- moved extdata/*csv to pRolocdata [2014-03-23 Sun]
- using *csv from pRolocdata [2014-03-23 Sun]
Changes in version 1.3.14
-------------------------
- deleted tab character [2014-03-15 Sat]
- added support for GMM parametrisation to phenoDisco [2014-03-17 Mon]
- message instead of warning when using colour and pch [2014-03-21 Fri]
- remove 1 duplicated mouse marker [2014-03-21 Fri]
Changes in version 1.3.13
-------------------------
- fixed a bug in addLegend [2014-03-14 Fri]
- updated testing to testthat 0.8 [2014-03-14 Fri]
- Fixing several warnings about symnbols being replaced upon pRoloc
loading and note about usage of ::: [2014-03-15 Sat]
Changes in version 1.3.12
-------------------------
- added phenoDisco2 for testing, allows choice of GMM
parameters [2014-02-26 Wed]
- removed duplicated fly markers [2014-02-28 Fri]
- updated affiliations in vignettes [2014-03-10 Mon]
Changes in version 1.3.11
-------------------------
- modify to new biocViews to DESCRIPTION file by s.arora [2014-03-04]
Changes in version 1.3.10
-------------------------
- new phenoDisco ndims argument to use more than two two principal
components as input for discovery analysis [2014-01-03 Mon]
- fixed and updated phenoDisco logging [2014-02-03 Mon]
- added support for parallel phenoDisco execution. See BPPARAM
argument [2014-02-03 Mon]
- fixed issues with using PD and ndims [2014-02-10 Mon]
- fixed call to anyUnknown in PD code [2014-02-10 Mon]
- checking if duplicated markers in addMarkers [2014-02-14 Fri]
Changes in version 1.3.9
------------------------
- bump to force rebuild for new Rcpp
Changes in version 1.3.8
------------------------
- Removed trailing space in mmus nucleus markers [2014-01-21 Tue]
- using filterNA to remove features with missing values
in plot2D [2014-01-21 Tue]
- fixed plot2D/addLegend [2014-01-23 Thu]
Changes in version 1.3.7
------------------------
- fixed addLegend to use correct colours (order) [2014-01-20 Mon]
- fix typo in addMarkers man [2014-01-20 Mon]
- re-arranged stockpch so that interleave full and empty
plotting character [2014-01-20 Mon]
- Removed last stockcol (tomato), too cose to "#FF7F00" [2014-01-20 Mon]
Changes in version 1.3.6
------------------------
- updated human markers: keep new pd.markers phenotypes,
validated by Lisa and remove singletons [2014-01-14 Tue]
- first stockpch is noe 19 [2014-01-16 Thu]
- plot2D(.., pch) now taken into account for labelled
data [2014-01-16 Thu]
- removed alpha plot2D argument [2014-01-17 Fri]
- updated plot2D and addLegend function with support for more
organelle groups than colours. The previous versions are
available as plot2D_v1 and addLegend_v1. [2014-01-17 Fri]
Changes in version 1.3.5
------------------------
- pRoloc citation [2014-01-12 Sun]
Changes in version 1.3.4
------------------------
- new unknownSet function [2013-12-11 Wed]
- updated vignettes to account for tan2009r1 changes [2013-12-16 Mon]
Changes in version 1.3.3
------------------------
- update citation in phenoDisco.Rd [2013-11-22 Fri]
- typos in vignettes [2013-11-25 Mon]
Changes in version 1.3.2
------------------------
- new markers [2013-11-06 Wed]
- markers in vinette [2013-11-15 Fri]
- mouse markers [2013-11-18 Mon]
Changes in version 1.3.1
------------------------
- using combineFeatures(..., na.rm=TRUE) in lopims pipeine [2013-10-22 Tue]
- corrected spelling errors in phenoDisco doc [2013-10-29 Tue]
Changes in version 1.3.0
------------------------
- next devel version fot Bioc 2.14
Changes in version 1.1.8
------------------------
- semi-sup and sup comparison sections in ml vig [2013-10-09 Wed]
Changes in version 1.1.7
------------------------
- getMarkers has names arg [2013-10-01 Tue]
Changes in version 1.1.6
------------------------
- new outliers arg to plot2D [2013-09-23 Mon]
- cite addMarkers in vignette [2013-09-26 Thu]