Creates a metaplot for comparing noise analysis results with RLBase

Plots the average standardized signal from noiseAnalyze alongside the samples in RLBase. For this plot, lower average signal indicates better signal to noise ratio. Note: This plot may be misleading if you supplied custom windows when running noiseAnalyze.

noiseComparisonPlot(object, mode = "auto", simple = TRUE, returnData = FALSE)

Arguments

object

An RLRanges object with noiseAnalyze already run.

mode

A character containing the R-loop data mode to compare against. See details for more information.

simple

A logical which specifies whether the plot should only show samples where the prediction and label are the same. Default: TRUE.

returnData

If TRUE, plot data is returned instead of plotting. Default: FALSE

Value

A ggplot2::ggplot object or a tbl if returnData is TRUE.

Details

Mode

The mode parameter specifies the R-loop modality to compare the user-supplied sample against in the plot. The default, "auto" specifies that the mode from the supplied RLRanges object will be used. Only one mode can be specified. For a list of applicable modes, see auxdata$available_modes.

Plot

The plot is a violin / jitter plot showing the distribution of average values from the noiseAnalyze output across RLBase samples of the selected mode. The user-supplied sample is annotated on the plot.

Examples

rlr <- readRDS(system.file("extdata", "rlrsmall.rds", package = "RLSeq"))

# Plot RL-Region overlap
noiseComparisonPlot(rlr)
#> see ?RLHub and browseVignettes('RLHub') for documentation
#> loading from cache
#> Warning: Removed 2 rows containing non-finite values (stat_boxplot).
#> Warning: Removed 2 rows containing missing values (geom_point).
#> Warning: Removed 2 rows containing missing values (geom_point).


# Return data only
noiseComparisonPlot(rlr, returnData = TRUE)
#> see ?RLHub and browseVignettes('RLHub') for documentation
#> loading from cache
#> # A tibble: 13 × 5
#>    sample         noise_index label prediction group        
#>    <chr>                <dbl> <chr> <chr>      <chr>        
#>  1 SRX1029475         0.0151  POS   POS        RDIP         
#>  2 SRX1029476         0.299   NEG   NEG        RDIP         
#>  3 SRX1029477         0.00545 POS   POS        RDIP         
#>  4 SRX1029478         0.149   NEG   NEG        RDIP         
#>  5 SRX4732954         0.0139  POS   NEG        RDIP         
#>  6 SRX4732955         0.0140  POS   NEG        RDIP         
#>  7 SRX4732956         0.0177  POS   NEG        RDIP         
#>  8 SRX4732957         0.0177  POS   NEG        RDIP         
#>  9 SRX3892923         0.00506 NEG   POS        RDIP         
#> 10 SRX6779957         0.00356 NEG   NEG        RDIP         
#> 11 SRX6779959         0.00515 NEG   NEG        RDIP         
#> 12 SRX7671349       NaN       NEG   NEG        RDIP         
#> 13 RDIP-Seq +RNH1   NaN       NEG   NEG        User-supplied