Add ggmuller plots

OncoSimulR/DESCRIPTION

@@ -29,7 +29,7 @@ License: GPL (>= 3)
 URL: https://github.com/rdiaz02/OncoSimul, https://popmodels.cancercontrol.cancer.gov/gsr/packages/oncosimulr/
 BugReports: https://github.com/rdiaz02/OncoSimul/issues
 Depends: R (>= 3.3.0)
-Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, nem
+Imports: Rcpp (>= 0.12.4), parallel, data.table, graph, Rgraphviz, gtools, igraph, methods, RColorBrewer, grDevices, car, dplyr, smatr, ggplot2, ggrepel, nem, ggmuller
 Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander
 LinkingTo: Rcpp
 VignetteBuilder: knitr

OncoSimulR/NAMESPACE

@@ -64,6 +64,7 @@ importFrom("dplyr", "full_join", "left_join", "right_join", "%>%", "mutate",
 importFrom("smatr", "ma") ## for major axis regression in some tests
 importFrom("car", "linearHypothesis")
 importFrom("nem", "transitive.reduction")
+importFrom("ggmuller", "get_Muller_df", "Muller_plot", "Muller_pop_plot")
 ## importFrom("slam", "simple_triplet_zero_matrix", ## "colapply_simple_triplet_matrix",
 ##            "col_sums")
 

OncoSimulR/R/stacked-plots.R

@@ -21,19 +21,19 @@
 
 
 
-## plot.stream makes a "stream plot" where each y series is plotted 
+## plot.stream makes a "stream plot" where each y series is plotted
 ## as stacked filled polygons on alternating sides of a baseline.
 
 ## Arguments include:
 ## 'x' - a vector of values
 ## 'y' - a matrix of data series (columns) corresponding to x
-## 'order.method' = c("as.is", "max", "first") 
+## 'order.method' = c("as.is", "max", "first")
 ##  "as.is" - plot in order of y column
 ##  "max" - plot in order of when each y series reaches maximum value
 ##  "first" - plot in order of when each y series first value > 0
 ## 'center' - if TRUE, the stacked polygons will be centered so that the middle,
-## i.e. baseline ("g0"), of the stream is approximately equal to zero. 
-## Centering is done before the addition of random wiggle to the baseline. 
+## i.e. baseline ("g0"), of the stream is approximately equal to zero.
+## Centering is done before the addition of random wiggle to the baseline.
 ## 'frac.rand' - fraction of the overall data "stream" range used to define the range of
 ## random wiggle (uniform distrubution) to be added to the baseline 'g0'
 ## 'spar' - setting for smooth.spline function to make a smoothed version of baseline "g0"
@@ -43,11 +43,11 @@
 ## '...' - other plot arguments
 
 plot.stream2 <- function(
-                        x, y, 
+                        x, y,
                         order.method = "as.is", frac.rand=0.1, spar=0.2,
                         center=TRUE,
-                        ylab="", xlab="",  
-                        border = NULL, lwd=1, 
+                        ylab="", xlab="",
+                        border = NULL, lwd=1,
                         col=rainbow(length(y[1,])),
                         ylim=NULL,
                         log = "",
@@ -60,7 +60,7 @@ plot.stream2 <- function(
     border <- as.vector(matrix(border, nrow=ncol(y), ncol=1))
     col <- as.vector(matrix(col, nrow=ncol(y), ncol=1))
     lwd <- as.vector(matrix(lwd, nrow=ncol(y), ncol=1))
-    
+
     if(order.method == "max") {
         ord <- order(apply(y, 2, which.max))
         y <- y[, ord]
@@ -98,7 +98,7 @@ plot.stream2 <- function(
     mid <- apply(outer.lims, 1,
                  function(r) mean(c(max(r, na.rm=TRUE),
                                     min(r, na.rm=TRUE)), na.rm=TRUE))
-    
+
     ## center and wiggle
     if(center) {
         g0 <- -mid + runif(length(x),
@@ -133,15 +133,13 @@ plot.stream2 <- function(
     }
 }
 
-
-
 ## plot.stacked makes a stacked plot where each y series is plotted on top
 ## of the each other using filled polygons
 
 ## Arguments include:
 ## 'x' - a vector of values
 ## 'y' - a matrix of data series (columns) corresponding to x
-## 'order.method' = c("as.is", "max", "first") 
+## 'order.method' = c("as.is", "max", "first")
 ##  "as.is" - plot in order of y column
 ##  "max" - plot in order of when each y series reaches maximum value
 ##  "first" - plot in order of when each y series first value > 0
@@ -151,10 +149,10 @@ plot.stream2 <- function(
 ## '...' - other plot arguments
 
 plot.stacked2 <- function(
-                         x, y, 
+                         x, y,
                          order.method = "as.is",
-                         ylab="", xlab="", 
-                         border = NULL, lwd=1, 
+                         ylab="", xlab="",
+                         border = NULL, lwd=1,
                          col=rainbow(length(y[1,])),
                          ylim=NULL,
                          log = "",

OncoSimulR/man/plot.oncosimul.Rd

@@ -16,7 +16,7 @@
   and clones with different number of drivers are plotted in different
   colours. Plots can alternatively display genotypes instead of drivers.
 
-  Plots available are line plots, stacked area, and stream plots.
+  Plots available are line plots, stacked area, stream plots and Muller plots.
 
 }
 
@@ -53,7 +53,9 @@
                            srange = c(0.4, 1),
                            vrange = c(0.8, 1),
                            breakSortColors = "oe",
-                           legend.ncols = "auto", ...)
+                           legend.ncols = "auto",
+                           muller.type = "frequency",
+                           ...)
 
 \method{plot}{oncosimulpop}(x,
                               ask = TRUE,
@@ -88,6 +90,7 @@
                               vrange = c(0.8, 1),
                               breakSortColors = "oe",
                               legend.ncols = "auto",
+                              muller.type = "frequency",
                               ...)
 
 }
@@ -109,22 +112,29 @@
     will be an unmanageable mess). The default is "drivers".
   }
 
-  \item{type}{One of "line", "stacked", "stream".
+  \item{type}{One of "line", "stacked", "stream", "muller".
 
     If "line", you are shown lines for each genotype or clone. This
     means that to get an idea of the total population size you need to
     use \code{plotDrivers = TRUE} with \code{addtot = TRUE}, or do the
     visual calculation in your head.
 
-    If "stacked" a stacked area plot. If "stream" a stream plot. Since
-  these stack areas, you immediately get the total population. But that
-  also means you cannot use \code{log}.
+    If "stacked" a stacked area plot. If "stream" a stream plot. If "muller" 
+    a Muller plot. Since these stack areas, you immediately get the total 
+    population. But that also means you cannot use \code{log}.
 
     The default is to use "line" for \code{show = "drivers"} and
     "stacked" for \code{show = "genotypes"}.
 
   }
 
+  \item{muller.type}{One of "frequency", "population".
+
+    If "frequency", it shows the frecuency of each clone. If "population"", 
+    shows changes in population sizes.
+
+    The default is to use "frequecy".
+  }
 
   \item{col}{ Colour of the lines/areas. For \code{show = "drivers"}
     each type of clone (where type is defined by number of drivers) has
@@ -306,7 +316,6 @@
   entries, and two for more than six.
 }
 
-
 
   \item{\dots}{
     Other arguments passed to \code{plots}. For instance, \code{main}.