inst/doc/Use_case.R

## ---- 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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QuantumClone documentation built on May 2, 2019, 3:03 a.m.