plot_dataset {ELBOW} | R Documentation

## plots data to see if it matches an elbow distribution.

### Description

A debug function for plotting data. This function plots an array or R object, and optionally draws the ELBOW limits on the plot. This function is mainly useful for the development and maintenance of the ELBOW method R package.

### Usage

      plot_dataset(my_data, column = NULL, upper_limit = NULL,
        lower_limit = NULL)

### Arguments

`my_data` | is the object, or array, to plot.
`column` | the column in the object/array to plot, if applicable.
`upper_limit` | the upper ELBOW limit for the data (optional)
`lower_limit` | the lower ELBOW limit for the data (optional)

### Examples

    # install the DESeq libraries
    		#if (!requireNamespace("BiocManager", quietly=TRUE))
        		#install.packages("BiocManager")
    		#BiocManager::install("DESeq")

    		## download the table
    		library("DESeq")

    		# the following bam file dataset was obtained from:
    		# http://cgrlucb.wikispaces.com/file/view/yeast_sample_data.txt
    		# it has been downloaded into this package for speed convenience.
    		filename <- system.file("extdata", "yeast_sample_data.txt", package = "ELBOW")

    		count_table <- read.table(filename, header=TRUE, sep="\t", row.names=1)
    		expt_design <- data.frame(row.names = colnames(count_table), condition = c("WE","WE","M","M","M"))
    		conditions = expt_design$condition
    		data <- newCountDataSet(count_table, conditions)
    		data <- estimateSizeFactors(data)
    		data <- as(data, "CountDataSet")
    		## data <- estimateVarianceFunctions(data)
    		data <- estimateDispersions(data)

    		# this next step is essential, but it takes a long time...
    		# so, just like a good cooking show we will skip this step
    		# and load a finished version.
    		#results <- nbinomTest(data, "M", "WE")

    		# The below two code lines load a copy of the above dataset
    		# which has already been processed by:
    		#     results <- nbinomTest(data, "M", "WE")
    		# For your own real data, you must use:
    		#     results <- nbinomTest(data, "M", "WE")'
    		# Instead of the two lines below:
    		data(yeast_nbinomTest_results, package="ELBOW")
    		results <- yeast_nbinomTest_results

    		# plot the results w/o elbow (useful if do_elbow doesn't work)
    		#plot_dataset(results, "log2FoldChange")

    		# plot the results w/elbow
    		limits <- do_elbow_rnaseq(results)
    		plot_dataset(results, "log2FoldChange", limits$up_limit, limits$low_limit)

[Package ELBOW version 1.18.1 Index]