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3.1.1: XOR, AND, OR: plots of DAGs honor all possible values

ramon diaz-uriarte (at Phelsuma) authored on 06/10/2021 18:38:06
Showing7 changed files

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@@ -1,8 +1,8 @@
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 Package: OncoSimulR
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 Type: Package
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 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 
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-Version: 3.1.0
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-Date: 2021-05-04
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+Version: 3.1.1
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+Date: 2021-10-06
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 Authors@R: c(
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 	      person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),	
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  	   		     email = "rdiaz02@gmail.com"),
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@@ -230,6 +230,9 @@ fast_peaks <- function(x, th) {
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                           th)]))
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 }
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+## FIXME! Unclear if we need the complete fitness matrix or if it will work with
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+## pieces (say, after removing those with fitness < WT, to try to make it faster
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+## and for general use in other cases)
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 ## wrapper to the C++ code
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 wrap_accessibleGenotypes <- function(x, th) {
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@@ -1511,8 +1511,15 @@ fitnessEffectsToIgraph <- function(rT, epistasis, orderEffects) {
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     g1 <- graph.data.frame(df)
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     E(g1)$color <- "black"
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+
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     E(g1)$color[E(g1)$typeDep == "SM"] <- "blue"
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+    E(g1)$color[E(g1)$typeDep == "OR"] <- "blue"
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+    E(g1)$color[E(g1)$typeDep == "semimonotone"] <- "blue"    
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+    
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     E(g1)$color[E(g1)$typeDep == "XMPN"] <- "red"
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+    E(g1)$color[E(g1)$typeDep == "XOR"] <- "red"
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+    E(g1)$color[E(g1)$typeDep == "xmpn"] <- "red"        
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+    
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     E(g1)$color[E(g1)$typeDep == "epistasis"] <- "orange"
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     E(g1)$color[E(g1)$typeDep == "orderEffect"] <- "orange"
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     E(g1)$lty <- 1
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@@ -1,3 +1,7 @@
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+Changes in version 3.1.1 (2021-10-06):
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+	- XOR, AND, OR dependencies: plots of DAGs honor all possible values.
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+	- Few miscell minor changes.
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+
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 Changes in version 3.0 (for BioC 3.13):
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 	- MAJOR change: frequency dependent fitness available.
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 	- Removed v.1 functionality.
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@@ -151,13 +151,26 @@ test_that("simple correct poset -> graph, 5 nodes, no root", {
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 test_that("to rT from poset, through adjmat with and w.o. root",
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           {
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-              expect_equal(
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+              ## Now, this fails with
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+              ## Error in `name %in% base || grepl("^%.*%$", name)`: 'length(x) = 3 > 1' in coercion to 'logical(1)'
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+              ## But all.equal does not break. So me thinks this is a problem in expect_equal
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+              ## and the new expect_waldo_equal.
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+              ## So I'll use all.equal.
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+              ## expect_equal(
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+              ##     OncoSimulR:::adjmat.to.restrictTable(
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+              ##         OncoSimulR:::posetToGraph(p5, names = 1:5, addroot = FALSE, type = "adjmat"),
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+              ##         root = FALSE),
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+              ##     OncoSimulR:::adjmat.to.restrictTable(
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+              ##         OncoSimulR:::posetToGraph(p5, names = 0:5, addroot = TRUE, type = "adjmat"),
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+              ##         root = TRUE))
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+              expect_true(all.equal(
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                   OncoSimulR:::adjmat.to.restrictTable(
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                       OncoSimulR:::posetToGraph(p5, names = 1:5, addroot = FALSE, type = "adjmat"),
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                       root = FALSE),
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                   OncoSimulR:::adjmat.to.restrictTable(
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                       OncoSimulR:::posetToGraph(p5, names = 0:5, addroot = TRUE, type = "adjmat"),
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-                      root = TRUE))
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+                      root = TRUE)
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+              ))
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           })
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@@ -7695,7 +7695,7 @@ small number of children via mutation to non-viable
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 "hybrids". Factor this into your equations for death rate, but this
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 should be negligible if death rate $\gg$ mutation rate. (You can
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 ameliorate this problem slightly by making mutation to the "species
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-indicator" locus very small, say $10^{10}$ ---do not set it to 0, as
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+indicator" locus very small, say $10^{-10}$ ---do not set it to 0, as
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 you will get an error).
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 Of course, you can extend the scheme above to arbitrary numbers of
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@@ -1,15 +1,15 @@
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 \usepackage[%
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-		shash={bb4ad3b},
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-		lhash={bb4ad3b194b97eba03a197a4e6d432f1a1e9167f},
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+		shash={f4285fb},
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+		lhash={f4285fb0479557c3f4d2b2f362703a464045bd2c},
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 		authname={ramon diaz-uriarte (at Phelsuma)},
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 		authemail={rdiaz02@gmail.com},
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-		authsdate={2021-04-27},
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-		authidate={2021-04-27 15:43:25 +0200},
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-		authudate={1619531005},
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+		authsdate={2021-09-01},
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+		authidate={2021-09-01 14:34:09 +0200},
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+		authudate={1630499649},
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 		commname={ramon diaz-uriarte (at Phelsuma)},
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 		commemail={rdiaz02@gmail.com},
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-		commsdate={2021-04-27},
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-		commidate={2021-04-27 15:43:25 +0200},
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-		commudate={1619531005},
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-		refnames={ (HEAD -> freq-dep-fitness, origin/rfitness_scale_3, rfitness_scale_3)}
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+		commsdate={2021-09-01},
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+		commidate={2021-09-01 14:34:09 +0200},
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+		commudate={1630499649},
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+		refnames={ (HEAD -> freq-dep-fitness, origin/freq-dep-fitness)}
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 	]{gitsetinfo}
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