generate_TMixClust_report {TMixClust} | R Documentation

## Generates a series of files containing a summary of the TMixClust analysis results

### Description

`generate_TMixClust_report`

### Usage

    generate_TMixClust_report(TMixClust_object, report_folder = paste(getwd(),
      "/TMixClust_report/", sep = ""), data_color = "#fd8d3c", x_label = "time",
      y_label = "value")

### Arguments

`TMixClust_object` | list object created by the `TMixClust` function (see function `TMixClust`)
`report_folder` | full path of the folder where the report files will be saved. Default is TMixClust_report/ folder in current working directory.
`data_color` | color of the time series to be used when generating the cluster plots. Default is orange.
`x_label` | label of the x axis for the cluster plots. Default is "time"
`y_label` | label of the y axis for the cluster plots. Default is "value"

### Value

Produces a series of files containing information about the clustering results and saves them in the provided folder location. The folder contains the following:

- `log-lihelihood.txt` - file with the log likelihood values at each iteration on separate lines

- `log-likelihood.pdf` - plot of log-likelihood at each iteration

- `posterior.txt` - file with the posterior probabilities of all the time-series for each cluster

- `estimated_curves/` - folder containing a number of files equal to the number of clusters; each file has 4 lines consisting of curve values and their confidence intervals (first 3 lines) for a discrete time grid (last line).

- `clusters/` - folder containing a plot with the time series in each cluster, a silhouette plot of the clustering configuration, as well as, for each cluster, a file containing the names of the time series in the respective cluster and a file containing the names and time series values for the time series in each cluster.

### Author(s)

Monica Golumbeanu, monica.golumbeanu@bsse.ethz.ch

### References

Golumbeanu M, Desfarges S, Hernandez C, Quadroni M, Rato S, Mohammadi P, Telenti A, Beerenwinkel N, Ciuffi A. (2017) Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection.

### Examples

    ## Not run:
    # Load the toy time series data provided with the TMixClust package
    data(toy_data_df)

    # Cluster the toy data with default parameters
    TMixClust_obj = TMixClust(toy_data_df)

    # Generate a TMixClust report in the current working directory
    generate_TMixClust_report(TMixClust_obj)

    ## End(Not run)

[Package TMixClust version 1.0.1 Index]