diff --git a/apple-touch-icon-120x120.png b/apple-touch-icon-120x120.png index bcbc9b83..3f2254bb 100644 Binary files a/apple-touch-icon-120x120.png and b/apple-touch-icon-120x120.png differ diff --git a/apple-touch-icon-152x152.png b/apple-touch-icon-152x152.png index c5ae05b7..9512ec89 100644 Binary files a/apple-touch-icon-152x152.png and b/apple-touch-icon-152x152.png differ diff --git a/apple-touch-icon-180x180.png b/apple-touch-icon-180x180.png index f0cea4e6..9a6edd2d 100644 Binary files a/apple-touch-icon-180x180.png and b/apple-touch-icon-180x180.png differ diff --git a/apple-touch-icon-60x60.png b/apple-touch-icon-60x60.png index 80e4bd6f..fa36cf59 100644 Binary files a/apple-touch-icon-60x60.png and b/apple-touch-icon-60x60.png differ diff --git a/apple-touch-icon-76x76.png b/apple-touch-icon-76x76.png index f0b739b1..64fad4b0 100644 Binary files a/apple-touch-icon-76x76.png and b/apple-touch-icon-76x76.png differ diff --git a/apple-touch-icon.png b/apple-touch-icon.png index 6a50c4dd..8cf6eb62 100644 Binary files a/apple-touch-icon.png and b/apple-touch-icon.png differ diff --git a/articles/mutations.html b/articles/mutations.html index 481a582c..5d96430a 100644 --- a/articles/mutations.html +++ b/articles/mutations.html @@ -138,8 +138,8 @@
MutationEng
#> Building context index...
#>
[█---------------------------------------] 0% [00m:00s] Processing chr. 22
- [█████████████████-----------------------] 40% [00m:01s] Processing chr. 22
- [█████████████████████████████████-------] 81% [00m:02s] Processing chr. 22
+ [████████████████████--------------------] 49% [00m:01s] Processing chr. 22
+ [████████████████████████████████████----] 89% [00m:02s] Processing chr. 22
[████████████████████████████████████████] 100% [00m:02s] Context index built
#>
[█---------------------------------------] 0% [00m:00s] Saving context index
@@ -815,8 +815,8 @@ Infinite Sites Modelphylo_forest2 <- m_engine$place_mutations(samples_forest, 1000)
#>
[█---------------------------------------] 0% [00m:00s] Placing mutations
- [████████████████████████----------------] 58% [00m:01s] Placing mutations
- [███████████████████████████████████████-] 95% [00m:02s] Placing mutations
+ [██████████████████████████--------------] 63% [00m:01s] Placing mutations
+ [███████████████████████████████████████-] 97% [00m:02s] Placing mutations
[████████████████████████████████████████] 100% [00m:02s] Mutations placed
# test whether the infinite sites conditions hold
@@ -840,7 +840,7 @@ Storing Phylogenetic Forestsloaded_phylo_forest <- load_phylogenetic_forest("phylo_forest.sff")
#>
[█---------------------------------------] 0% [00m:00s] Loading forest
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+ [███████████████████████████████████-----] 87% [00m:01s] Loading forest
[████████████████████████████████████████] 100% [00m:01s] Forest loaded
loaded_phylo_forest
diff --git a/articles/sampling.html b/articles/sampling.html
index 71595271..5b98ed94 100644
--- a/articles/sampling.html
+++ b/articles/sampling.html
@@ -288,7 +288,7 @@ Randomised multi-region samples
sim$run_up_to_size("B", 10000)
#>
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+ [█████████-------------------------------] 21% [00m:00s] Cells: 144065
[████████████████████████████████████████] 100% [00m:00s] Saving snapshot
current <- plot_tissue(sim)
@@ -406,21 +406,19 @@ Two populations with epigenetic s
# let it grow more time units
sim$run_up_to_time(sim$get_clock() + 25)
#>
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- [████████████████████████████████████████] 100% [00m:11s] Saving snapshot
-
-plot_tissue(sim, num_of_bins = 500)
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+ [████████████████████████████████████████] 100% [00m:09s] Saving snapshot
+
+plot_tissue(sim, num_of_bins = 500)
Sample again and plot the tissue
diff --git a/articles/sequencing.html b/articles/sequencing.html index 64fa28cf..1837b35f 100644 --- a/articles/sequencing.html +++ b/articles/sequencing.html @@ -105,7 +105,7 @@Sequencing Simulationphylo_forest <- load_phylogenetic_forest("phylo_forest.sff") #> [█---------------------------------------] 0% [00m:00s] Loading forest - [████████████████████████████████████----] 89% [00m:01s] Loading forest + [███████████████████████████████████-----] 86% [00m:01s] Loading forest [████████████████████████████████████████] 100% [00m:01s] Forest loaded phylo_forest @@ -127,83 +127,82 @@
Sequencing Simulation#> [█---------------------------------------] 0% [00m:00s] Found 22 [█---------------------------------------] 0% [00m:00s] Reading 22 - [█---------------------------------------] 0% [00m:00s] Reading 22 + [█---------------------------------------] 0% [00m:01s] Reading 22 [█---------------------------------------] 0% [00m:01s] Processing chr. 22 - [█---------------------------------------] 0% [00m:01s] Processing chr. 22 - [███-------------------------------------] 5% [00m:02s] Processing chr. 22 - [████------------------------------------] 9% [00m:03s] Processing chr. 22 - [██████----------------------------------] 13% [00m:04s] Processing chr. 22 - [███████---------------------------------] 17% [00m:05s] Processing chr. 22 - [█████████-------------------------------] 22% [00m:06s] Processing chr. 22 - [███████████-----------------------------] 26% [00m:07s] Processing chr. 22 - [█████████████---------------------------] 30% [00m:08s] Processing chr. 22 - [██████████████--------------------------] 34% [00m:09s] Processing chr. 22 - [████████████████------------------------] 38% [00m:10s] Processing chr. 22 - [█████████████████-----------------------] 42% [00m:11s] Processing chr. 22 - [███████████████████---------------------] 45% [00m:12s] Processing chr. 22 - [████████████████████--------------------] 49% [00m:13s] Processing chr. 22 - [██████████████████████------------------] 52% [00m:14s] Processing chr. 22 - [███████████████████████-----------------] 56% [00m:15s] Processing chr. 22 - [████████████████████████----------------] 58% [00m:16s] Processing chr. 22 - [██████████████████████████--------------] 63% [00m:17s] Processing chr. 22 - [███████████████████████████-------------] 66% [00m:18s] Processing chr. 22 - [█████████████████████████████-----------] 70% [00m:19s] Processing chr. 22 - [██████████████████████████████----------] 73% [00m:20s] Processing chr. 22 - [███████████████████████████████---------] 76% [00m:21s] Processing chr. 22 - [█████████████████████████████████-------] 80% [00m:22s] Processing chr. 22 - [██████████████████████████████████------] 84% [00m:23s] Processing chr. 22 - [████████████████████████████████████----] 88% [00m:24s] Processing chr. 22 - [█████████████████████████████████████---] 91% [00m:25s] Processing chr. 22 - [███████████████████████████████████████-] 95% [00m:26s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:27s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:28s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:29s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:30s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:31s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:32s] Processing chr. 22 - [████████████████████████████████████████] 99% [00m:33s] Processing chr. 22 - [████████████████████████████████████████] 100% [00m:35s] Read simulated - -# let us load the dplyr library to filter the `simulate_seq` output -library(dplyr) -#> -#> Attaching package: 'dplyr' -#> The following objects are masked from 'package:stats': -#> -#> filter, lag -#> The following objects are masked from 'package:base': -#> -#> intersect, setdiff, setequal, union - -seq_results %>% head -#> chr chr_pos ref alt causes classes S_1_1.occurrences S_1_1.coverage -#> 1 22 10510210 N C A driver 1 2 -#> 2 22 12028576 N G B driver 0 2 -#> 3 22 16051493 G A <NA> germinal 2 3 -#> 4 22 16052080 G A <NA> germinal 2 3 -#> 5 22 16053659 A C <NA> germinal 3 3 -#> 6 22 16053863 G A <NA> germinal 1 2 -#> S_1_1.VAF S_1_2.occurrences S_1_2.coverage S_1_2.VAF S_2_1.occurrences -#> 1 0.5000000 2 6 0.3333333 0 -#> 2 0.0000000 0 4 0.0000000 3 -#> 3 0.6666667 0 1 0.0000000 2 -#> 4 0.6666667 2 4 0.5000000 3 -#> 5 1.0000000 5 5 1.0000000 1 -#> 6 0.5000000 0 2 0.0000000 2 -#> S_2_1.coverage S_2_1.VAF S_2_2.occurrences S_2_2.coverage S_2_2.VAF -#> 1 3 0.00 1 3 0.3333333 -#> 2 3 1.00 0 1 0.0000000 -#> 3 5 0.40 0 1 0.0000000 -#> 4 4 0.75 1 1 1.0000000 -#> 5 1 1.00 3 3 1.0000000 -#> 6 2 1.00 1 2 0.5000000 -#> normal_sample.occurrences normal_sample.coverage normal_sample.VAF -#> 1 0 1 0.0 -#> 2 0 2 0.0 -#> 3 2 4 0.5 -#> 4 1 2 0.5 -#> 5 2 2 1.0 -#> 6 3 3 1.0
The function simulate_seq()
returns a data frame whose
rows represent the mutations observed in the simulated reads (currently,
only SNVs are supported).
Each SAM file contains the reads produced by simulating the
sequencing of all the samples. The command-line tools samtools
can be used to
split the reads by sample.
When the output directory already contains a SAM file associated with a chromosome, the alignments on that chromosome are saved in a file whose name is the first available, having the format diff --git a/articles/tissue_simulation.html b/articles/tissue_simulation.html index cf11afba..e6a78d83 100644 --- a/articles/tissue_simulation.html +++ b/articles/tissue_simulation.html @@ -543,7 +543,7 @@
At this point, we can inspect in more details the tissue. It can help to facet on the species to clearly appreciate the spatial diffusion of @@ -712,20 +712,19 @@
plot_state(sim)
The time-series can be plot using plot_timeseries()
.
# Time-series plot
@@ -979,10 +977,10 @@ Time-Varying Evolutionary Rates# Now D will become larger
sim$run_up_to_size("D+", 6000)
#>
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[████████████████████████████████████████] 100% [00m:03s] Saving snapshot
# Current state
@@ -1020,9 +1018,6 @@ Time-Varying Evolutionary Rates ggplot2::xlim(clock * 3/4, clock) +
ggplot2::scale_y_log10()