1. OncoSimulR
  2. tests
  3. testthat
  4. test.plotFitnessLandscape.R
Browse code

3.99.1: interventions, death with fdf, user variables

ramon diaz-uriarte (at Phelsuma) authored on 25/06/2022 14:24:13
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ 79ffadf
... ... 
@@ -29,7 +29,7 @@ test_that("Exercise plotting and dealing with different matrix input", {
29 29
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     m88 <- cbind(B = c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
31 31 
     suppressWarnings(expect_identical(as.data.frame(
32 
-        evalAllGenotypes(allFitnessEffects(genotFitness = m88),
32 
+        evalAllGenotypes(allFitnessEffects(genotFitness = m88, frequencyDependentFitness = FALSE),
33 33 
                                       addwt = TRUE)),
34 34 
                      data.frame(Genotype = c("WT", "A", "B", "A, B"),
35 35 
                                 Fitness = c(1, 3, 2, 5.5),
Browse code

v. 2.99.3

ramon diaz-uriarte (at Phelsuma) authored on 13/12/2020 14:35:47
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ 8d0896d
... ... 
@@ -28,12 +28,13 @@ test_that("Exercise plotting and dealing with different matrix input", {
28 28 
                    "One column named ''", fixed = TRUE)
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     m88 <- cbind(B = c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
31 
-    expect_identical(as.data.frame(
31 
+    suppressWarnings(expect_identical(as.data.frame(
32 32 
         evalAllGenotypes(allFitnessEffects(genotFitness = m88),
33 33 
                                       addwt = TRUE)),
34 34 
                      data.frame(Genotype = c("WT", "A", "B", "A, B"),
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                                 Fitness = c(1, 3, 2, 5.5),
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                                 stringsAsFactors = FALSE))
37 
+    )
37 38 
     expect_warning(plotFitnessLandscape(m88),
38 39 
                    "One column named ''", fixed = TRUE)
39 40
... ... 
@@ -45,15 +46,16 @@ test_that("Exercise plotting and dealing with different matrix input", {
45 46
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     expect_silent(plot(evalAllGenotypes(fe, order = FALSE)))
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49 
+
48 50 
     ## same as
49 51 
     expect_silent(plotFitnessLandscape(evalAllGenotypes(fe, order = FALSE)))
50 52 
     ## more ggrepel
51 53 
     expect_silent(plot(evalAllGenotypes(fe, order = FALSE), use_ggrepel = TRUE))
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53 55 
     m98 <- cbind(B = c(2, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
54 
-    expect_error(allFitnessEffects(genotFitness = m98),
56 
+    suppressWarnings(expect_error(allFitnessEffects(genotFitness = m98),
55 57 
                  "First ncol - 1 entries not in ",
56 
-                 fixed = TRUE)
58 
+                 fixed = TRUE))
57 59 
 })
58 60
59 61
... ... 
@@ -83,6 +85,7 @@ test_that("to_FitnessMatrix stops as it should", {
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84 86
85 87 
 test_that("to_FitnessMatrix can deal with df", {
88 
+    suppressWarnings({
86 89 
     m4 <- data.frame(G = c("A, B", "A", "WT", "B"),
87 90 
                      Fitness = c(3, 2, 1, 4))
88 91 
     expect_message(OncoSimulR:::to_Fitness_Matrix(m4, 2000),
... ... 
@@ -106,6 +109,7 @@ test_that("to_FitnessMatrix can deal with df", {
106 109 
     expect_message(plotFitnessLandscape(x3))
107 110 
     expect_message(plotFitnessLandscape(m5))
108 111 
     expect_message(plotFitnessLandscape(m4))
112 
+    })
109 113 
 })
110 114
111 115
Browse code

2.9.9

ramon diaz-uriarte (at Phelsuma) authored on 17/04/2018 23:58:39
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ e719a81
... ... 
@@ -1,3 +1,4 @@
1 
+inittime <- Sys.time()
1 2 
 ## This actually tests much more than plotFitnessLandscape
2 3 
 cat(paste("\n Starting plotFitnessLandscape at", date()))
3 4 
 test_that("Exercise plotting and dealing with different matrix input", {
... ... 
@@ -740,3 +741,5 @@ test_that("Some random checks of the fast peaks function", {
740 741 
     }
741 742 
 })
742 743 
 cat(paste("\n Ending plotFitnessLandscape at", date()), "\n")
744 
+cat(paste("  Took ", round(difftime(Sys.time(), inittime, units = "secs"), 2), "\n\n"))
745 
+rm(inittime)
Browse code

v. 2.9.2 - LOD: using only the strict Szendro et al. meaning. - POM: computed in C++. - Using fitness landscape directly when given as input (no conversion to epistasis)

ramon diaz-uriarte (at Phelsuma) authored on 24/11/2017 12:41:48
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ ab43994
... ... 
@@ -1,3 +1,5 @@
1 
+## This actually tests much more than plotFitnessLandscape
2 
+cat(paste("\n Starting plotFitnessLandscape at", date()))
1 3 
 test_that("Exercise plotting and dealing with different matrix input", {
2 4 
     r1 <- rfitness(4)
3 5 
     expect_silent(plot(r1))
... ... 
@@ -12,15 +14,27 @@ test_that("Exercise plotting and dealing with different matrix input", {
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13 15 
     m6 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))
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     expect_message(plotFitnessLandscape(m6),
15 
-                   "Setting/resetting gene names because", fixed = TRUE)
17 
+                   "No column names:", fixed = TRUE)
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19 
+    ## the next are so ill formed that they should not be accepted
17 20 
     m7 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
18 
-    expect_message(plotFitnessLandscape(m7),
19 
-                   "Setting/resetting gene names because", fixed = TRUE)
21 
+    expect_error(plotFitnessLandscape(m7),
22 
+                    "duplicated column names", fixed = TRUE)
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24 
+    ## zz: why isn't this working?
21 25 
     m8 <- cbind(A = c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
22 
-    expect_message(plotFitnessLandscape(m8),
23 
-                   "Setting/resetting gene names because", fixed = TRUE)
26 
+    expect_warning(plotFitnessLandscape(m8),
27 
+                   "One column named ''", fixed = TRUE)
28 
+
29 
+    m88 <- cbind(B = c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
30 
+    expect_identical(as.data.frame(
31 
+        evalAllGenotypes(allFitnessEffects(genotFitness = m88),
32 
+                                      addwt = TRUE)),
33 
+                     data.frame(Genotype = c("WT", "A", "B", "A, B"),
34 
+                                Fitness = c(1, 3, 2, 5.5),
35 
+                                stringsAsFactors = FALSE))
36 
+    expect_warning(plotFitnessLandscape(m88),
37 
+                   "One column named ''", fixed = TRUE)
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26 40 
     ## Specify fitness with allFitnessEffects, and plot it
... ... 
@@ -34,6 +48,11 @@ test_that("Exercise plotting and dealing with different matrix input", {
34 48 
     expect_silent(plotFitnessLandscape(evalAllGenotypes(fe, order = FALSE)))
35 49 
     ## more ggrepel
36 50 
     expect_silent(plot(evalAllGenotypes(fe, order = FALSE), use_ggrepel = TRUE))
51 
+
52 
+    m98 <- cbind(B = c(2, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
53 
+    expect_error(allFitnessEffects(genotFitness = m98),
54 
+                 "First ncol - 1 entries not in ",
55 
+                 fixed = TRUE)
37 56 
 })
38 57
39 58
... ... 
@@ -720,3 +739,4 @@ test_that("Some random checks of the fast peaks function", {
720 739 
         }
721 740 
     }
722 741 
 })
742 
+cat(paste("\n Ending plotFitnessLandscape at", date()), "\n")
Browse code

version 2.7.2 Changes in version 2.7.2 (2017-09-27): - genot_to_adj_mat in C++. - fast_peaks (for no backmutation cases). - Better explanation and testing of peaks and valleys. - Clarified simOGraph transitive reduction. - Better handling of ti corner cases. - Magellan reading fuctions adapted to output of newer (as of 2017-07) version of Magellan. - sorting gene names in allGenotypes_to_matrix. - sampledGenotypes: genotype names with sorted gene names.

ramon diaz-uriarte (at Phelsuma) authored on 27/09/2017 10:23:50
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ f9a38e2
... ... 
@@ -272,3 +272,451 @@ test_that("internal peak valley functions", {
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274 274 
 })
275 
+
276 
+
277 
+## Beware that using peak_valley on only_accessible makes a difference
278 
+test_that("internal peak valley functions w/wo inaccessible filter", {
279 
+    ## A is accessible, a peak
280 
+    ## AB is a peak if only forward. But there is no
281 
+    ## reciprocal sign epistasis here!
282 
+
283 
+    ## We want peaks in general, not just
284 
+    ## under assumption of "no back mutation"?
285 
+
286 
+    ## Well, no, that is not obvious with cancer progression models if we
287 
+    ## do not allow back mutations.
288 
+
289 
+    ## We get a different result when we restrict to accessible
290 
+    ## because all < 0 in adjacency are turned to NAs.
291 
+
292 
+    ## Thinking in terms of adjacency matrix, AB is not a peak if it has a
293 
+    ## positive and a negative entry in its column, because the negative
294 
+    ## entry means there is an ancestor with larger fitness.
295 
+    ## But see below for why plainly using the adjacency matrix can give bad results.
296 
+
297 
+    ## The next matrices are all fitness matrix. Last column is fitness.
298 
+    mf1 <- rbind(
299 
+        c(0, 0, 1),
300 
+        c(1, 0, 4),
301 
+        c(0, 1, 2),
302 
+        c(1, 1, 3)
303 
+    )
304 
+
305 
+    plotFitnessLandscape(mf1)
306 
+
307 
+    expect_equal(
308 
+        OncoSimulR:::peak_valley(
309 
+                                OncoSimulR:::genot_to_adj_mat(mf1))$peak, 2)
310 
+
311 
+    expect_equal(
312 
+            OncoSimulR:::peak_valley(
313 
+                             OncoSimulR:::filter_inaccessible(
314 
+                                              OncoSimulR:::genot_to_adj_mat(mf1), 0))$peak,
315 
+        c(2, 4))
316 
+
317 
+    expect_equal(
318 
+        OncoSimulR:::fast_peaks(mf1, 0),
319 
+        c(2, 4))
320 
+
321 
+
322 
+    ## reorder the rows of the matrix. Affects fast_peaks, as it should
323 
+    mf1 <- rbind(
324 
+        c(1, 0, 4),
325 
+        c(0, 0, 1),
326 
+        c(1, 1, 3),
327 
+        c(0, 1, 2)
328 
+    )
329 
+
330 
+    plotFitnessLandscape(mf1)
331 
+    ## this is not affected, since it uses, by construction, the ordered matrix
332 
+    expect_equal(
333 
+        OncoSimulR:::peak_valley(
334 
+                                OncoSimulR:::genot_to_adj_mat(mf1))$peak, 2)
335 
+    ## ditto
336 
+    expect_equal(
337 
+            OncoSimulR:::peak_valley(
338 
+                             OncoSimulR:::filter_inaccessible(
339 
+                                              OncoSimulR:::genot_to_adj_mat(mf1), 0))$peak,
340 
+        c(2, 4))
341 
+    expect_equal(
342 
+        OncoSimulR:::fast_peaks(mf1, 0),
343 
+        c(1, 3))
344 
+
345 
+
346 
+
347 
+    ## filtering by inaccessible also likely gets rid of all
348 
+    ## peaks in the non-accessible part of the fitness landscape.
349 
+    ## But of course those cannot be peaks, since they are inaccessible
350 
+
351 
+    mf3 <- rbind(
352 
+        c(0, 0, 0, 1),
353 
+        c(1, 0, 0, 2),
354 
+        c(0, 1, 0, 0.1),
355 
+        c(0, 0, 1, 0.3),
356 
+        c(1, 1, 0, 3),
357 
+        c(1, 0, 1, 4),
358 
+        c(0, 1, 1, 0.4),
359 
+        c(1, 1, 1, 0.2)
360 
+    )
361 
+
362 
+    ## plotFitnessLandscape(mf3)
363 
+    ## BC is detected as a peak, the seventh entry
364 
+    expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf3))$peak,
365 
+                 c(5, 6, 7))
366 
+
367 
+    ## recall this gives the columns of the reduced matrix, which are the former
368 
+    ## 5 and 6
369 
+    expect_equal(OncoSimulR:::peak_valley(
370 
+                                  OncoSimulR:::filter_inaccessible(
371 
+                                                   OncoSimulR:::genot_to_adj_mat(mf3), 0))$peak,
372 
+                 c(3, 4))
373 
+
374 
+    ## correct indices from original matrix
375 
+    expect_equal(
376 
+        OncoSimulR:::fast_peaks(mf3, 0),
377 
+        c(5, 6))
378 
+
379 
+    ## works under reorder?
380 
+    expect_equal(
381 
+        OncoSimulR:::fast_peaks(mf3[c(5, 1, 2, 3, 7, 4, 6), ], 0),
382 
+        c(1, 7))
383 
+
384 
+
385 
+
386 
+
387 
+    mf4 <- rbind(
388 
+        c(0, 0, 0, 1),
389 
+        c(1, 0, 0, 2),
390 
+        c(0, 1, 0, 0.1),
391 
+        c(0, 0, 1, 0.3),
392 
+        c(1, 1, 0, 3),
393 
+        c(1, 0, 1, 4),
394 
+        c(0, 1, 1, 0.4),
395 
+        c(1, 1, 1, 1.2)
396 
+    )
397 
+
398 
+    ## plotFitnessLandscape(mf4)
399 
+
400 
+    ## ABC is not detected as a peak, because it is not.
401 
+    ## Issue is not its accessibility, but that AC and AB have larger fitness
402 
+    ## see example with mf5
403 
+    expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf4))$peak,
404 
+                 c(5, 6))
405 
+
406 
+    ## recall this gives the columns of the reduced matrix, which are the former
407 
+    ## 5 and 6
408 
+    expect_equal(OncoSimulR:::peak_valley(
409 
+                                  OncoSimulR:::filter_inaccessible(
410 
+                                                   OncoSimulR:::genot_to_adj_mat(mf4), 0))$peak,
411 
+                 c(3, 4))
412 
+
413 
+    expect_equal(
414 
+        OncoSimulR:::fast_peaks(mf4, 0),
415 
+        c(5, 6))
416 
+
417 
+
418 
+    ## Now ABC is accessible
419 
+      mf5 <- rbind(
420 
+        c(0, 0, 0, 1),
421 
+        c(1, 0, 0, 2),
422 
+        c(0, 1, 0, 0.1),
423 
+        c(0, 0, 1, 0.3),
424 
+        c(1, 1, 0, 3),
425 
+        c(1, 0, 1, 4),
426 
+        c(0, 1, 1, 0.4),
427 
+        c(1, 1, 1, 3.5)
428 
+    )
429 
+
430 
+      ## plotFitnessLandscape(mf5)
431 
+      ## plotFitnessLandscape(mf5, only_accessible = TRUE)
432 
+
433 
+      ## But only AC is the peak, correctly
434 
+      expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf5))$peak,
435 
+                   c(6))
436 
+
437 
+      ## Now, both AC and ABC are peaks
438 
+      ## columns 4 and 5 correspond to genotypes 6 and 8
439 
+      expect_equal(OncoSimulR:::peak_valley(
440 
+                                    OncoSimulR:::filter_inaccessible(
441 
+                                                     OncoSimulR:::genot_to_adj_mat(mf5), 0))$peak,
442 
+                   c(4, 5))
443 
+
444 
+      expect_equal(
445 
+          OncoSimulR:::fast_peaks(mf5, 0),
446 
+          c(6, 8))
447 
+
448 
+    ## AC and ABC same max fitness
449 
+      mf6 <- rbind(
450 
+        c(0, 0, 0, 1),
451 
+        c(1, 0, 0, 2),
452 
+        c(0, 1, 0, 0.1),
453 
+        c(0, 0, 1, 0.3),
454 
+        c(1, 1, 0, 3),
455 
+        c(1, 0, 1, 4),
456 
+        c(0, 1, 1, 0.4),
457 
+        c(1, 1, 1, 4)
458 
+    )
459 
+
460 
+      ## plotFitnessLandscape(mf6)
461 
+      ## Both AC and ABC are peaks. Correctly
462 
+      expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf6))$peak,
463 
+                   c(6, 8))
464 
+
465 
+      ## fast peaks should refuse to run
466 
+      expect_error(
467 
+          OncoSimulR:::fast_peaks(mf6, 0),
468 
+          "There could be several connected maxima",
469 
+          fixed = TRUE)
470 
+
471 
+
472 
+
473 
+      ## A and AC
474 
+      mf7 <- rbind(
475 
+        c(0, 0, 0, 1),
476 
+        c(1, 0, 0, 4),
477 
+        c(0, 1, 0, 0.1),
478 
+        c(0, 0, 1, 0.3),
479 
+        c(1, 1, 0, 3),
480 
+        c(1, 0, 1, 4),
481 
+        c(0, 1, 1, 0.4),
482 
+        c(1, 1, 1, 3.4)
483 
+    )
484 
+      ## plotFitnessLandscape(mf7)
485 
+      ## Both A and AC are peaks. Correctly
486 
+      expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf7))$peak,
487 
+                   c(2, 6))
488 
+
489 
+      ## fast peaks should refuse to run
490 
+      expect_error(
491 
+          OncoSimulR:::fast_peaks(mf7, 0),
492 
+          "There could be several connected maxima",
493 
+          fixed = TRUE)
494 
+
495 
+
496 
+
497 
+      ## A, AC, ABC same max fitness
498 
+      mf8 <- rbind(
499 
+        c(0, 0, 0, 1),
500 
+        c(1, 0, 0, 4),
501 
+        c(0, 1, 0, 0.1),
502 
+        c(0, 0, 1, 0.3),
503 
+        c(1, 1, 0, 3),
504 
+        c(1, 0, 1, 4),
505 
+        c(0, 1, 1, 0.4),
506 
+        c(1, 1, 1, 4)
507 
+    )
508 
+      ## plotFitnessLandscape(mf8)
509 
+      ## Both A and AC are peaks. Correctly
510 
+      expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf8))$peak,
511 
+                   c(2, 6, 8))
512 
+
513 
+
514 
+      ## fast peaks should refuse to run
515 
+      expect_error(
516 
+          OncoSimulR:::fast_peaks(mf8, 0),
517 
+          "There could be several connected maxima",
518 
+          fixed = TRUE)
519 
+
520 
+      ## A, AC, AB same max fitness
521 
+      mf9 <- rbind(
522 
+        c(0, 0, 0, 1),
523 
+        c(1, 0, 0, 4),
524 
+        c(0, 1, 0, 0.1),
525 
+        c(0, 0, 1, 0.3),
526 
+        c(1, 1, 0, 4),
527 
+        c(1, 0, 1, 4),
528 
+        c(0, 1, 1, 0.4),
529 
+        c(1, 1, 1, 2.4)
530 
+    )
531 
+      ## plotFitnessLandscape(mf9, use_ggrepel = TRUE)
532 
+      ## Both A and AC are peaks. Correctly
533 
+      expect_equal(OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(mf9))$peak,
534 
+                   c(2, 5, 6))
535 
+
536 
+
537 
+
538 
+      ## This illustrates that the "filter_inaccessible" is not just "do
539 
+      ## not take into account inaccessible genotypes" but, properly, do
540 
+      ## not take into account, do not allow any travelling through
541 
+      ## inaccessible paths.
542 
+
543 
+      ## Thus, filter_inaccessible is the way to go if we want to exclude
544 
+      ## backmutation. In no bakcmutation, it is not possible to go from
545 
+      ## m+1 to m mutations.
546 
+
547 
+      ## It also shows that naively looking at the adjacency matrix can
548 
+      ## fail. Two reasons:
549 
+
550 
+      ## a) the last row will never have any entries and yet it need not
551 
+      ## be a peak.
552 
+
553 
+      ## b) simply looking at adjacency matrix is not the correct
554 
+      ## procedure when some fitnesses can be equal. That is what the
555 
+      ## function peak_valley works hard to get right :-)
556 
+
557 
+
558 
+    cp2 <- structure(c(0, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0,
559 
+0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1,
560 
+1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
561 
+0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
562 
+1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1,
563 
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1,
564 
+1, 1, 1, 1, 0, 1, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1,
565 
+1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0,
566 
+0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0,
567 
+0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0,
568 
+0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0,
569 
+1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0,
570 
+1, 1, 1, 1, 1, 0, 1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0,
571 
+0, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0,
572 
+1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1,
573 
+1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1, 1,
574 
+1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1,
575 
+1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1,
576 
+0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 1,
577 
+0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 1, 0,
578 
+0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0,
579 
+0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 0, 0, 1, 1, 1, 0, 0, 0,
580 
+1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1,
581 
+1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1,
582 
+1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0,
583 
+0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0,
584 
+0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 0, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0,
585 
+1, 1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0, 1,
586 
+1, 0, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0,
587 
+1, 1, 1, 0, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 0, 1, 1, 1, 0, 1, 1,
588 
+1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 1,
589 
+0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0,
590 
+1, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 0, 1, 0, 0, 1, 0, 0,
591 
+1, 0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 0, 1, 0, 0, 1,
592 
+0, 1, 0, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 0, 1, 1,
593 
+0, 1, 1, 1, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 1,
594 
+1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0,
595 
+0, 0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1,
596 
+0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0,
597 
+1, 0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 1,
598 
+0, 0, 1, 0, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0, 0, 1, 0, 1,
599 
+1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 0, 1, 1, 1, 0,
600 
+1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0.852873407703003,
601 
+1.51520969989942, 1.09934414414554, 1.08362391548151, 1.06352377058758,
602 
+0.875558455823467, 1.69351291065104, 2.92492684398312, 1.02057836095586,
603 
+0.994559647972076, 1.01807462848707, 0.782398502758159, 0.755318352952028,
604 
+1.81553780643735, 1.7427209966816, 1.00116069406198, 0.790243245268257,
605 
+3.38168029927183, 1.18573953796889, 1.24679706264807, 0.944183929293486,
606 
+1.04153712305771, 1.20232261789798, 1.0345783487807, 1.04678440594199,
607 
+0.993244793867836, 0.97914067773803, 0.79321495112376, 0.868101325153957,
608 
+0.866235177920767, 4.1155779007473, 3.163209721772, 4.34977195536485,
609 
+1.09932137400121, 1.08612305022998, 0.916953742980573, 0.850115441923501,
610 
+1.06277833622263, 0.865087563773651, 0.928169473201598, 0.904902930158639,
611 
+0.897493717866434, 0.71149600120298, 1.06538015204221, 1.07859259299858,
612 
+0.858803230350538, 2.25551012930227, 1.09241633274047, 0.870425423271033,
613 
+2.17687545546796, 0.84459090869647, 4.58149975106353, 3.85245245151455,
614 
+1.28342034151899, 1.08529050597462, 1.02256835452167, 1.04982916832593,
615 
+1.0457848642841, 0.90107628754529, 1.08969768294891, 1.05766476796899,
616 
+0.902394628842996, 0.888348932462492, 1.01037474862489, 0.954093541062801,
617 
+0.807820459139572, 2.74832174163312, 1.01318977068049, 0.854004033396404,
618 
+0.842034005421367, 0.800544915243185, 5.31108977064723, 5.31423066433053,
619 
+1.16539625099584, 0.983449927610599, 0.996320237843515, 0.9794158873742,
620 
+1.02038748073625, 0.808875731463122, 0.964868528161141, 0.966566509486774,
621 
+0.860373057266184, 0.81168825662344, 1.19978481918247, 0.98157798351476,
622 
+0.999463234369357, 0.98711106267367, 0.961995700808845, 4.79391503400402,
623 
+0.998909701750288, 0.996465768481649, 0.785688019266101, 0.778917380394268,
624 
+1.17230915723272, 1.19911647477422, 0.961939861987872, 0.981542927739855,
625 
+0.999822362533057, 1.15236749698624, 0.919688401637553, 0.876733220798505,
626 
+0.92069327916386, 0.958801043337062, 0.670589798279379, 0.84152795885645,
627 
+5.93895353544503, 0.723329951949942, 0.733188455582477, 1.07557023464861,
628 
+1.09180382079188, 0.923957719945906, 0.93313538716072, 0.896562810368268,
629 
+1.09769821865825, 1.10615389985864, 0.94426955155254, 0.898545873061366,
630 
+0.876269943340891, 1.11556411094416, 0.94930544641744, 1.02495854041569,
631 
+0.794907983845338, 0.847332095413669, 0.776896984008625, 0.928896557877041,
632 
+0.945135371172636, 0.892100531723894), .Dim = c(128L, 8L), .Dimnames = list(
633 
+    NULL, c("CDKN2A", "KRAS", "MLL3", "PXDN", "SMAD4", "TGFBR2",
634 
+    "TP53", "")))
635 
+
636 
+    expect_equal(length(
637 
+        OncoSimulR:::peak_valley(OncoSimulR:::genot_to_adj_mat(cp2))$peak), 4)
638 
+
639 
+    expect_equal(length(
640 
+        OncoSimulR:::peak_valley(
641 
+                         OncoSimulR:::filter_inaccessible(
642 
+                                          OncoSimulR:::genot_to_adj_mat(cp2), 0))$peak), 6)
643 
+
644 
+
645 
+    expect_equal(
646 
+          OncoSimulR:::fast_peaks(cp2, 0),
647 
+        c(51, 55, 68, 74, 90, 107))
648 
+
649 
+    ## Nope, since filter inaccessible removes genotypes
650 
+    expect_false(all(
651 
+        OncoSimulR:::peak_valley(
652 
+                         OncoSimulR:::filter_inaccessible(
653 
+                                          OncoSimulR:::genot_to_adj_mat(cp2), 0))$peak ==
654 
+        OncoSimulR:::fast_peaks(cp2, 0)))
655 
+
656 
+
657 
+    ## compare with the probl
658 
+    gnn <- OncoSimulR:::to_Fitness_Matrix(cp2, 1000)$afe[, "Genotype"]
659 
+
660 
+    plotFitnessLandscape(cp2, use_ggrepel = TRUE, only_accessible = TRUE)
661 
+
662 
+    expect_equal(
663 
+        gnn[OncoSimulR:::fast_peaks(cp2, 0)],
664 
+        c("KRAS, PXDN, TP53",
665 
+          "MLL3, PXDN, SMAD4",
666 
+          "CDKN2A, KRAS, MLL3, TP53",
667 
+          "CDKN2A, KRAS, TGFBR2, TP53",
668 
+          "KRAS, MLL3, TGFBR2, TP53",
669 
+          "CDKN2A, KRAS, PXDN, SMAD4, TP53"))
670 
+
671 
+    ## can also check by removing the inacessible genotypes so the indices are the same
672 
+    agg <- OncoSimulR:::wrap_accessibleGenotypes(cp2, 0)
673 
+    cp3 <- cp2[agg, ]
674 
+
675 
+    ## This is NOT correct: we have removed the inacessible,
676 
+    ## but we allow backmutation
677 
+    ## OncoSimulR:::peak_valley(
678 
+    ##                  OncoSimulR:::genot_to_adj_mat(cp3))$peak
679 
+
680 
+    expect_equal(OncoSimulR:::peak_valley(
681 
+                     OncoSimulR:::filter_inaccessible(
682 
+                                      OncoSimulR:::genot_to_adj_mat(cp3), 0))$peak,
683 
+                 OncoSimulR:::fast_peaks(cp3, 0))
684 
+
685 
+    gnn3 <- gnn[agg]
686 
+
687 
+    expect_equal(
688 
+        gnn3[OncoSimulR:::fast_peaks(cp3, 0)],
689 
+        c("KRAS, PXDN, TP53",
690 
+          "MLL3, PXDN, SMAD4",
691 
+          "CDKN2A, KRAS, MLL3, TP53",
692 
+          "CDKN2A, KRAS, TGFBR2, TP53",
693 
+          "KRAS, MLL3, TGFBR2, TP53",
694 
+          "CDKN2A, KRAS, PXDN, SMAD4, TP53"))
695 
+
696 
+
697 
+})
698 
+
699 
+
700 
+
701 
+test_that("Some random checks of the fast peaks function", {
702 
+    niter <- 50
703 
+    for(i in 1:niter) {
704 
+        for(ng in 2:6) {
705 
+            rtmp <- rfitness(ng)
706 
+            p1 <- OncoSimulR:::peak_valley(
707 
+                                   OncoSimulR:::filter_inaccessible(
708 
+                                                    OncoSimulR:::genot_to_adj_mat(rtmp), 0))$peak
709 
+            expect_equal(length(p1),
710 
+                         length(OncoSimulR:::fast_peaks(rtmp, 0)))
711 
+            agg <- OncoSimulR:::wrap_accessibleGenotypes(rtmp, 0)
712 
+            if(length(agg) >= 2) {
713 
+                ## cat(".")
714 
+                p2 <- OncoSimulR:::peak_valley(
715 
+                                       OncoSimulR:::filter_inaccessible(
716 
+                                                        OncoSimulR:::genot_to_adj_mat(rtmp[agg, , drop = FALSE]), 0))$peak
717 
+                expect_equal(p2, OncoSimulR:::fast_peaks(rtmp[agg, , drop = FALSE], 0))
718 
+                expect_equal(length(p2), length(p1))
719 
+            }
720 
+        }
721 
+    }
722 
+})
Browse code

v.2.3.7; detectionProb mechanism;\n documentation enhancements;\n more tests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@119150 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 05/07/2016 15:59:56
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ 4d70b94
... ... 
@@ -1,4 +1,4 @@
1 
-test_that("Exercise plotting", {
1 
+test_that("Exercise plotting and dealing with different matrix input", {
2 2 
     r1 <- rfitness(4)
3 3 
     expect_silent(plot(r1))
4 4 
     expect_silent(plot(r1, log = TRUE))
... ... 
@@ -7,8 +7,21 @@ test_that("Exercise plotting", {
7 7
8 8
9 9 
     ## Specify fitness in a matrix, and plot it
10 
-    m5 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))
10 
+    m5 <- cbind(A = c(0, 1, 0, 1), B = c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
11 11 
     expect_silent(plotFitnessLandscape(m5))
12 
+
13 
+    m6 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))
14 
+    expect_message(plotFitnessLandscape(m6),
15 
+                   "Setting/resetting gene names because", fixed = TRUE)
16 
+
17 
+    m7 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
18 
+    expect_message(plotFitnessLandscape(m7),
19 
+                   "Setting/resetting gene names because", fixed = TRUE)
20 
+
21 
+    m8 <- cbind(A = c(0, 1, 0, 1), c(0, 0, 1, 1), F = c(1, 2, 3, 5.5))
22 
+    expect_message(plotFitnessLandscape(m8),
23 
+                   "Setting/resetting gene names because", fixed = TRUE)
24 
+
12 25
13 26 
     ## Specify fitness with allFitnessEffects, and plot it
14 27 
     fe <- allFitnessEffects(epistasis = c("a : b" = 0.3,
... ... 
@@ -33,6 +46,18 @@ test_that("to_FitnessMatrix stops as it should", {
33 46 
     expect_error(OncoSimulR:::to_Fitness_Matrix(x2, 2000),
34 47 
                  "We cannot guess what you are passing",
35 48 
                  fixed = TRUE)
49 
+    ## This is done above
50 
+    ## g <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1))
51 
+    ## s1 <- c(1, 1.4, 1.2, 1.5)
52 
+    ## expect_error(OncoSimulR:::to_Fitness_Matrix(cbind(g, s1), 2000),
53 
+    ##              "Matrix x must have column names",
54 
+    ##              fixed = TRUE)
55 
+    ## expect_message(plotFitnessLandscape(cbind(g, s1)),
56 
+    ##              "Matrix x must have column names",
57 
+    ##              fixed = TRUE)
58 
+    ## expect_message(plotFitnessLandscape(cbind(g, A = c(1, 2))),
59 
+    ##              "Matrix x must have column names",
60 
+    ##              fixed = TRUE)
36 61 
 })
37 62
38 63
Browse code

v.2.3.6;\n improved test coverage

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@118947 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 25/06/2016 16:08:52
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ df13108
... ... 
@@ -1,6 +1,10 @@
1 1 
 test_that("Exercise plotting", {
2 2 
     r1 <- rfitness(4)
3 3 
     expect_silent(plot(r1))
4 
+    expect_silent(plot(r1, log = TRUE))
5 
+    expect_silent(plot(r1, log = TRUE, use_ggrepel = TRUE))
6 
+    expect_silent(plot(r1, log = TRUE, show_labels = FALSE))
7 
+
4 8
5 9 
     ## Specify fitness in a matrix, and plot it
6 10 
     m5 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))
... ... 
@@ -12,14 +16,54 @@ test_that("Exercise plotting", {
12 16 
                             noIntGenes = c("e" = 0.1))
13 17
14 18 
     expect_silent(plot(evalAllGenotypes(fe, order = FALSE)))
15 
-
19 
+
16 20 
     ## same as
17 21 
     expect_silent(plotFitnessLandscape(evalAllGenotypes(fe, order = FALSE)))
18 
-
22 
+    ## more ggrepel
23 
+    expect_silent(plot(evalAllGenotypes(fe, order = FALSE), use_ggrepel = TRUE))
24 
+})
25 
+
26 
+
27 
+test_that("to_FitnessMatrix stops as it should", {
28 
+    x1 <- data.frame(a = 1:2, b = 1:2)
29 
+    expect_error(OncoSimulR:::to_Fitness_Matrix(x1, 2000),
30 
+                 "We cannot guess what you are passing",
31 
+                 fixed = TRUE)
32 
+    x2 <- list(a = 12, b = 13)
33 
+    expect_error(OncoSimulR:::to_Fitness_Matrix(x2, 2000),
34 
+                 "We cannot guess what you are passing",
35 
+                 fixed = TRUE)
19 36 
 })
20 37
21 38
22 39
40 
+test_that("to_FitnessMatrix can deal with df", {
41 
+    m4 <- data.frame(G = c("A, B", "A", "WT", "B"),
42 
+                     Fitness = c(3, 2, 1, 4))
43 
+    expect_message(OncoSimulR:::to_Fitness_Matrix(m4, 2000),
44 
+                   "Column names of object", fixed = TRUE)
45 
+    m5 <- data.frame(G = c("A, B", "B"),
46 
+                     Fitness = c(3, 2))
47 
+    expect_message(OncoSimulR:::to_Fitness_Matrix(m5, 2000),
48 
+                   "Column names of object", fixed = TRUE)
49 
+    x1 <- data.frame(a = c("A, B"), Fitness = 2)
50 
+    expect_message(OncoSimulR:::to_Fitness_Matrix(x1, 2000),
51 
+                   "Column names of object", fixed = TRUE)
52 
+    x2 <- data.frame(a = c("A, B", "B"), Fitness = c(2, 3))
53 
+    expect_message(OncoSimulR:::to_Fitness_Matrix(x2, 2000),
54 
+                   "Column names of object", fixed = TRUE)
55 
+    x3 <- data.frame(a = c("A, B", "C"), Fitness = c(2, 3))
56 
+    expect_message(OncoSimulR:::to_Fitness_Matrix(x3, 2000),
57 
+                   "Column names of object", fixed = TRUE)
58 
+    ## Now, the user code
59 
+    expect_message(plotFitnessLandscape(x1))
60 
+    expect_message(plotFitnessLandscape(x2))
61 
+    expect_message(plotFitnessLandscape(x3))
62 
+    expect_message(plotFitnessLandscape(m5))
63 
+    expect_message(plotFitnessLandscape(m4))
64 
+})
65 
+
66 
+
23 67 
 test_that("internal peak valley functions", {
24 68
25 69 
     x <- matrix(NA, 14, 14)
Browse code

v. 2.3.3.\n mutator, fitness landscapes, rfitness, and many other changes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OncoSimulR@118909 bc3139a8-67e5-0310-9ffc-ced21a209358

Ramon Diaz-Uriarte authored on 23/06/2016 16:43:51
Showing 1 changed files
tests/testthat/test.plotFitnessLandscape.R
History View file @ 50a9420
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,205 @@
1 
+test_that("Exercise plotting", {
2 
+    r1 <- rfitness(4)
3 
+    expect_silent(plot(r1))
4 
+
5 
+    ## Specify fitness in a matrix, and plot it
6 
+    m5 <- cbind(c(0, 1, 0, 1), c(0, 0, 1, 1), c(1, 2, 3, 5.5))
7 
+    expect_silent(plotFitnessLandscape(m5))
8 
+
9 
+    ## Specify fitness with allFitnessEffects, and plot it
10 
+    fe <- allFitnessEffects(epistasis = c("a : b" = 0.3,
11 
+                                          "b : c" = 0.5),
12 
+                            noIntGenes = c("e" = 0.1))
13 
+
14 
+    expect_silent(plot(evalAllGenotypes(fe, order = FALSE)))
15 
+
16 
+    ## same as
17 
+    expect_silent(plotFitnessLandscape(evalAllGenotypes(fe, order = FALSE)))
18 
+
19 
+})
20 
+
21 
+
22 
+
23 
+test_that("internal peak valley functions", {
24 
+
25 
+    x <- matrix(NA, 14, 14)
26 
+    x[1, 3] <- -2
27 
+    x[1, 2] <- -4
28 
+    x[2, 3] <- 5
29 
+    x[3, 4] <- 0
30 
+    x[4, 5] <- 0
31 
+    x[5, 6] <- 4
32 
+    x[3, 7] <- -3
33 
+    x[7, 8] <- 0
34 
+    x[3, 10] <- -4
35 
+    x[10, 11] <- -4
36 
+    x[11, 12] <- 0
37 
+    x[12, 13] <- 3
38 
+    x[8, 9] <- 5
39 
+    x[12, 14] <- -5
40 
+
41 
+    (pv <-  OncoSimulR:::peak_valley(x))
42 
+    expect_equal(c(1, 6, 9, 13), pv$peak)
43 
+    expect_equal(c(2, 7, 8, 14), pv$valley)
44 
+
45 
+    x <- matrix(NA, 15, 15)
46 
+    x[1, 3] <- -2
47 
+    x[1, 2] <- -4
48 
+    x[2, 3] <- 5
49 
+    x[3, 4] <- 0
50 
+    x[4, 5] <- 0
51 
+    x[5, 6] <- 4
52 
+    x[3, 7] <- -3
53 
+    x[7, 8] <- 0
54 
+    x[3, 10] <- -4
55 
+    x[10, 11] <- -4
56 
+    x[11, 12] <- 0
57 
+    x[12, 13] <- 3
58 
+    x[8, 9] <- 5
59 
+    x[12, 14] <- -5
60 
+    x[14, 15] <- 2
61 
+
62 
+    (pv <-  OncoSimulR:::peak_valley(x))
63 
+    expect_equal(c(1, 6, 9, 13, 15), pv$peak)
64 
+    expect_equal(c(2, 7, 8, 14), pv$valley)
65 
+
66 
+
67 
+    x <- matrix(NA, 15, 15)
68 
+    x[1, 3] <- -2
69 
+    x[1, 2] <- -4
70 
+    x[2, 3] <- 5
71 
+    x[3, 4] <- 3
72 
+    x[4, 5] <- 0
73 
+    x[5, 6] <- 4
74 
+    x[3, 7] <- -3
75 
+    x[7, 8] <- 0
76 
+    x[3, 10] <- -4
77 
+    x[10, 11] <- -4
78 
+    x[11, 12] <- 0
79 
+    x[12, 13] <- 3
80 
+    x[8, 9] <- 5
81 
+    x[12, 14] <- -5
82 
+    x[14, 15] <- 2
83 
+
84 
+    (pv <-  OncoSimulR:::peak_valley(x))
85 
+    expect_equal(c(1, 6, 9, 13, 15), pv$peak)
86 
+    expect_equal(c(2, 7, 8, 14), pv$valley)
87 
+
88 
+
89 
+
90 
+    x <- matrix(NA, 15, 15)
91 
+    x[1, 3] <- -2
92 
+    x[1, 2] <- -4
93 
+    x[2, 3] <- 5
94 
+    x[3, 4] <- 3
95 
+    x[4, 5] <- -1
96 
+    x[5, 6] <- 4
97 
+    x[3, 7] <- -3
98 
+    x[7, 8] <- 0
99 
+    x[3, 10] <- -4
100 
+    x[10, 11] <- -4
101 
+    x[11, 12] <- 0
102 
+    x[12, 13] <- 3
103 
+    x[8, 9] <- 5
104 
+    x[12, 14] <- -5
105 
+    x[14, 15] <- 2
106 
+
107 
+    (pv <-  OncoSimulR:::peak_valley(x))
108 
+    expect_equal(c(1, 4, 6, 9, 13, 15), pv$peak)
109 
+    expect_equal(c(2, 5, 7, 8, 14), pv$valley)
110 
+
111 
+
112 
+    x <- matrix(NA, 15, 15)
113 
+    x[1, 3] <- -2
114 
+    x[1, 2] <- -4
115 
+    x[2, 3] <- 5
116 
+    x[3, 4] <- 3
117 
+    x[4, 5] <- -1
118 
+    x[5, 6] <- 4
119 
+    x[3, 7] <- -3
120 
+    x[7, 8] <- 0
121 
+    x[3, 10] <- -4
122 
+    x[10, 11] <- -4
123 
+    x[11, 12] <- 0
124 
+    x[12, 13] <- 3
125 
+    x[8, 9] <- 5
126 
+    x[12, 14] <- -5
127 
+    x[14, 15] <- 2
128 
+    x[2, 7] <- 1
129 
+
130 
+    (pv <-  OncoSimulR:::peak_valley(x))
131 
+    expect_equal(c(1, 4, 6, 9, 13, 15), pv$peak)
132 
+    expect_equal(c(2, 5, 14), pv$valley)
133 
+
134 
+
135 
+
136 
+    x <- matrix(NA, 15, 15)
137 
+    x[1, 3] <- -2
138 
+    x[1, 2] <- -4
139 
+    x[2, 3] <- 5
140 
+    x[3, 4] <- 0
141 
+    x[4, 5] <- -1
142 
+    x[5, 6] <- 4
143 
+    x[3, 7] <- -3
144 
+    x[7, 8] <- 0
145 
+    x[3, 10] <- -4
146 
+    x[10, 11] <- -4
147 
+    x[11, 12] <- 0
148 
+    x[12, 13] <- 3
149 
+    x[8, 9] <- 5
150 
+    x[12, 14] <- -5
151 
+    x[14, 15] <- 2
152 
+    x[2, 7] <- 1 ## hummm.. 3 and 4 should be a peak?Nope, from 1
153 
+
154 
+    (pv <-  OncoSimulR:::peak_valley(x))
155 
+    expect_equal(c(1, 6, 9, 13, 15), pv$peak)
156 
+    expect_equal(c(2, 5, 14), pv$valley)
157 
+
158 
+
159 
+    x <- matrix(NA, 15, 15)
160 
+    x[1, 3] <- 1
161 
+    x[1, 2] <- -4
162 
+    x[2, 3] <- 5
163 
+    x[3, 4] <- 0
164 
+    x[4, 5] <- -1
165 
+    x[5, 6] <- 4
166 
+    x[3, 7] <- -3
167 
+    x[7, 8] <- 0
168 
+    x[3, 10] <- -4
169 
+    x[10, 11] <- -4
170 
+    x[11, 12] <- 0
171 
+    x[12, 13] <- 3
172 
+    x[8, 9] <- 5
173 
+    x[12, 14] <- -5
174 
+    x[14, 15] <- 2
175 
+    x[2, 7] <- 1
176 
+
177 
+    (pv <-  OncoSimulR:::peak_valley(x))
178 
+    expect_equal(c(3, 4, 6, 9, 13, 15), pv$peak)
179 
+    expect_equal(c(2, 5, 14), pv$valley)
180 
+
181 
+
182 
+
183 
+    x <- matrix(NA, 5, 5)
184 
+    x[1, 3] <- -2
185 
+    x[2, 3] <- 4
186 
+    x[3, 4] <- 0
187 
+    x[4, 5] <- 6
188 
+
189 
+    (pv <-  OncoSimulR:::peak_valley(x))
190 
+    expect_equal(c(1, 5), pv$peak)
191 
+    expect_equal(c(2), pv$valley)
192 
+
193 
+
194 
+    x <- matrix(NA, 5, 5)
195 
+    x[1, 3] <- -2
196 
+    x[2, 3] <- -5
197 
+    x[3, 4] <- 0
198 
+    x[4, 5] <- 6