Nothing
## ---- include = FALSE----------------------------------------------------
library(QuantumClone)
knitr::opts_chunk$set(collapse = TRUE, fig.width = 7, fig.height = 7,
fig.align = "center",
fig.dpi = 96)
## ----QuantumCat_example, eval = FALSE------------------------------------
# # Example was generated calling:
# Input_Example<-QuantumCat(number_of_clones = 4,
# number_of_mutations = 100,
# ploidy = "AB",depth = 150,
# number_of_samples = 2,
# contamination = c(0,0))
## ----echo=FALSE----------------------------------------------------------
knitr::kable(head(QuantumClone::Input_Example[[1]]))
## ----One_step_example, eval = FALSE--------------------------------------
# One_step_clustering(SNV_list = Input_Example, FREEC_list = NULL, contamination = c(0,0),
# nclone_range = 2:5, clone_priors = NULL, prior_weight = NULL,
# Initializations = 1 , preclustering = "Flash",
# simulated = FALSE, epsilon = 5 * (10^(-3)),
# save_plot = TRUE, ncores = 1,
# restrict.to.AB = FALSE, output_directory = NULL)
## ----out,echo= FALSE-----------------------------------------------------
knitr::kable(head(QuantumClone::QC_output$filtered.data[[1]]))
## ----plot, echo= FALSE,warning=FALSE-------------------------------------
QuantumClone::plot_QC_out(QuantumClone::QC_output)
## ----multiplot, echo= FALSE,warning=FALSE--------------------------------
modQCout<-QuantumClone::QC_output
modQCout$filtered.data[[3]]<-modQCout$filtered.data[[1]]
QuantumClone::plot_QC_out(modQCout,Sample_names=c("Diag","Rel","Metastasis"),sample_selected = 1:3)
## ----margin, echo= FALSE,warning=FALSE-----------------------------------
QuantumClone::plot_with_margins_densities(QuantumClone::QC_output)
## ----evol, echo = FALSE, warning = FALSE---------------------------------
QuantumClone::evolution_plot(QuantumClone::QC_output,Sample_names = c("Timepoint_1","Timepoint_2"))
## ----Tree, echo = TRUE, warning = FALSE,eval=TRUE------------------------
Cellularities<-cbind(QuantumClone::QC_output$EM.output$centers[[1]],QuantumClone::QC_output$EM.output$centers[[2]])
Tree<-QuantumClone::Tree_generation(Cellularities)
## ----ShowTree, echo = FALSE----------------------------------------------
knitr::kable(Tree[[1]][[1]])
## ----TreePlot, echo = TRUE, warning = FALSE,eval=TRUE--------------------
QuantumClone::multiplot_trees(Tree,d = 4)
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