analyzeBasesPlotOnly {BBCAnalyzer} | R Documentation

## Plots the number of reads at all previously defined positions

### Description

To allow for a quick change in the way the analysis of the bases, deletions and insertions at defined positions in sequence alignment data is visualized, the function `analyzeBasesPlotOnly` may be used. It solely performs the last step of the whole analysis pipeline – the plotting of the results.

### Usage

    analyzeBasesPlotOnly(sample_names, vcf_input, output, known_file,
                         output_list, qual_lower_bound, qual_upper_bound,
                         marks, relative, per_sample)

### Arguments

`sample_names` | The file containing the names of the samples to be analyzed.
`vcf_input` | The folder containing the vcf files or a VcfFileList of the samples to be analyzed or a multiple-sample vcf file. The argument may be left blank.
`output` | The folder to write the output (plots) into. The argument may be left blank. In this case, the plots are returned to the workspace.
`known_file` | The name of a tabix file containing e.g. known polymorphisms or mutations (dbSNP). The argument may be left blank.
`output_list` | The name of the list that is returned by the function `analyzeBases`.
`qual_lower_bound` | The lower bound for the mean quality that shall be color-coded in the plots. All bases with a mean quality below `qual_lower_bound` are colored with the lightest color defined for the corresponding base. If the bases shall not be color-coded according to their mean quality, `qual_lower_bound` has to be identical compared to `qual_upper_bound`.
`qual_upper_bound` | The upper bound for the mean quality that shall be color-coded in the plots. All bases with a mean quality above `qual_upper_bound` are colored with the darkest color defined for the corresponding base. If the bases shall not be color-coded according to their mean quality, `qual_upper_bound` has to be identical compared to `qual_lower_bound`.
`marks` | A vector of floats [0,1] defining the levels at which marks shall be drawn in the plot.
`relative` | A boolean defining whether the relative (`true`) or the absolute (`false`) number of reads shall be plotted.
`per_sample` | A boolean defining whether one plot per sample (`true`) or one plot per target (`false`) shall be created.

### Details

About the input:

Names of the samples to be analyzed have to be provided by a file (`sample_names`). There has to be one sample name per line without the ".bam"-suffix.

If vcf files shall be considered, the corresponding files of the samples to be analyzed have to be provided in a folder (`vcf_input`). There has to be one file per sample. The names of the files have to match the sample names provided by `sample_names`. If a vcf file is not available for one or more samples, empty vcf files may be used instead.

The value that gets returned by the function `analyzeBases` has to be provided (`output_list`). Otherwise, `analyzeBasesPlotOnly` will not be able to use the previously generated output.

About plotting the results:

The absolute number of the detected bases, deletions and insertions for each sample at each targeted position is plotted if `relative==FALSE`. Otherwise the relative frequencies of the detected bases, deletions and insertions for each sample at each targeted position get plotted. The bars are colored according to the base (adenine: green; cytosine: blue; guanine: yellow; thymine: red; deletion: black; insertion: lilac edge) and their mean quality (high mean quality: dark color; low mean quality: light color). The reference bases (using the defined package `ref_genome`) are plotted on the negative y-axis below each position. If a file containing known variants or mutations is provided (`known_file`), more than one reference base is plotted at the corresponding position. For each position to be analyzed, lines are drawn at the heights of the ratios defined in `marks`. Every targeted position is labelled according to the chromosome and the position. The function copes with different inserted bases at one position (stacked bars) and insertions $>$1bp, even if these are not covered by all samples. If the analysis shall consider vcf files as well (`vcf_input` not blank), the expected number of detected bases, deletions and insertions – according to the vcf file – is added to the plot using dashed lines.

Plot per sample: One barplot per sample is created. The output is saved as [Sample].png.

Plot per target: One barplot per targeted position is created. The output is saved as chr[number];[position].png.

### Value

No value is returned.

### Author(s)

Sarah Sandmann <sarah.sandmann@uni-muenster.de>

### References

db SNP – Short Genetic variations: http://www.ncbi.nlm.nih.gov/SNP/

### See Also

`BBCAnalyzer`, `analyzeBases`

### Examples

    library("BSgenome.Hsapiens.UCSC.hg19")
    ref_genome<-BSgenome.Hsapiens.UCSC.hg19

    output<-analyzeBases(sample_names=system.file("extdata","SampleNames_small.txt",package="BBCAnalyzer"),
                         bam_input=system.file("extdata",package="BBCAnalyzer"),
                         target_regions=system.file("extdata","targetRegions_small.txt",package="BBCAnalyzer"),
                         vcf_input="",
                         output=system.file("extdata",package="BBCAnalyzer"),
                         output_pictures=system.file("extdata",package="BBCAnalyzer"),
                         known_file="",
                         genome=ref_genome,
                         MQ_threshold=60,
                         BQ_threshold=50,
                         frequency_threshold=0.01,
                         qual_lower_bound=58,
                         qual_upper_bound=63,
                         marks=c(0.01),
                         relative=TRUE,
                         per_sample=TRUE)

    analyzeBasesPlotOnly(sample_names=system.file("extdata","SampleNames_small.txt",package="BBCAnalyzer"),
                         vcf_input="",
                         output=system.file("extdata",package="BBCAnalyzer"),
                         known_file="",
                         output_list=output,
                         qual_lower_bound=58,
                         qual_upper_bound=63,
                         marks=c(0.25,0.5,0.75,1),
                         relative=FALSE,
                         per_sample=TRUE)

[Package BBCAnalyzer version 1.12.0 Index]