shinyPlot_SNPindex: Shiny: Plot SNP-indices
In EG-lisy/BSAvis: Bulk Segregant Analysis - Visualisation Package

Please note that this function is not to be run manually. Creates plots specific to the R-shiny application, showing (for each bulk, or just one of them) the mean SNP-index values against the mid position of the corresponding window of a specific chromosome.

1	shinyPlot_SNPindex(vcf.df.window.SNPindex, chr, bulk, ranges)

`chr`	chrosome ID
`bulk`	bulk/bulks to take into consideration when plotting
`ranges`	axes ranges (x,y)
`SNPindex.windows`	filtered data frame (containing both bulks)

This function is a variant of the plot_SNPindex() function created to meet the needs of the R-shiny application. Firstly, a ggplot object is created with all the necessary plotting elements, exept for the lines specific for each bulk (corresponding to mean SNP-index against the mid position of the corresponding window of a specific chromosome). Based on the value of the bulk argument, a SNP-index line/s will be added to the previously created ggplotobject.

If bulk=0, two lines corresponding to the SNP-indices of both wild-type and mutant bulks will be added. If bulk=1 or bulk=2, a single line will be added to the plot, respectively corresponding to the wild-type or mutant bulk SNP-indices.

The value of the bulk parameter will be set inside the R-shiny application function (BSAvis_shiny()) depending on the user's interactive-input. Additionally, this function includes a "ranges" argument that allows setting the limits of the x and y-axis, to show a zoomed area of the SNP-index plot when selected. If no area is selected, the x and y axis limits will be set to null, showing the entire plot.

This function does not include any arguments related to plot saving since this functionality is linked to a saving button found inside the BSAvis R-Shiny application.

EG-lisy/BSAvis documentation built on Dec. 17, 2021, 5:38 p.m.