diff --git a/404.html b/404.html index 0311f41..0c3d93b 100644 --- a/404.html +++ b/404.html @@ -20,7 +20,7 @@ wigglescout - 0.18.1 + 0.19.0 + + + + + +
+
+
+ +

Density plot of a precalculated GRanges object

+ Source: R/bwplot.R +
plot_gr_density.Rd
+
+ +
+

Plots a density plot from two mcols of a GRanges object files that were +already calculated using bw_loci or bw_bins

+
+ +
+

Usage

+ 
plot_gr_density(
+  gr,
+  x,
+  y,
+  plot_binwidth = 0.05,
+  remove_top = 0,
+  verbose = TRUE,
+  selection = NULL
+)
+
+ +
+

Arguments

+ + +
gr
+

Scored GRanges object

+ + +
x
+

Column in gr corresponding to the x axis

+ + +
y
+

Column in gr corresponding to the y axis.

+ + +
plot_binwidth
+

Resolution of the bins in the density histogram +(different to genomic bin size)

+ + +
remove_top
+

Return range 0-(1-remove_top). By default returns the +whole distribution (remove_top == 0).

+ + +
verbose
+

Put a caption with relevant parameters on the plot.

+ + +
selection
+

A GRanges object to restrict binning to a certain set of +intervals. This is useful for debugging and improving performance of +locus specific analyses.

+ +
+
+

Value

+

A ggplot object.

+
+ +
+ + +
+ + + + + + + diff --git a/reference/plot_gr_scatter.html b/reference/plot_gr_scatter.html new file mode 100644 index 0000000..d01e3fa --- /dev/null +++ b/reference/plot_gr_scatter.html @@ -0,0 +1,147 @@ + +Scatterplot of a precalculated GRanges object — plot_gr_scatter • wigglescout + Skip to contents + + +
+
+
+ +

Scatterplot of a precalculated GRanges object

+ Source: R/bwplot.R +
plot_gr_scatter.Rd
+
+ +
+

Plots a scatter plot from two mcols of a GRanges object files and an optional +set of BED files as highlighted annotations. Bins are highlighted if there is +at least minoverlap base pairs overlap with any loci in BED file.

+
+ +
+

Usage

+ 
plot_gr_scatter(
+  gr,
+  x,
+  y,
+  highlight = NULL,
+  minoverlap = 0L,
+  highlight_label = NULL,
+  highlight_colors = NULL,
+  remove_top = 0,
+  verbose = TRUE,
+  selection = NULL
+)
+
+ +
+

Arguments

+ + +
gr
+

Scored GRanges object

+ + +
x
+

Column in gr corresponding to the x axis

+ + +
y
+

Column in gr corresponding to the y axis.

+ + +
highlight
+

List of bed files to use as highlight for subgroups.

+ + +
minoverlap
+

Minimum overlap required for a bin to be highlighted

+ + +
highlight_label
+

Labels for the highlight groups. +If not provided, filenames are used.

+ + +
highlight_colors
+

Array of color values for the highlighting groups

+ + +
remove_top
+

Return range 0-(1-remove_top). By default returns the +whole distribution (remove_top == 0).

+ + +
verbose
+

Put a caption with relevant parameters on the plot.

+ + +
selection
+

A GRanges object to restrict binning to a certain set of +intervals. This is useful for debugging and improving performance of +locus specific analyses.

+ +
+
+

Value

+

A ggplot object.

+
+
+

Details

+

If specifying minoverlap, you must take into account the bin_size parameter +and the size of the loci you are providing as BED file.

+

This function does not calculate background normalization or anything, you +can do that in the prior call to bw_bins or bw_loci

+
+ +
+ + +
+ + + + + + + diff --git a/reference/plot_gr_violin.html b/reference/plot_gr_violin.html new file mode 100644 index 0000000..2177eb9 --- /dev/null +++ b/reference/plot_gr_violin.html @@ -0,0 +1,134 @@ + +Violin plot of a precalculated GRanges object — plot_gr_violin • wigglescout + Skip to contents + + +
+
+
+ +

Violin plot of a precalculated GRanges object

+ Source: R/bwplot.R +
plot_gr_violin.Rd
+
+ +
+

Plots a violin plot of bin distribution of a set of bigWig files optionally +overlaid with annotated bins. Bins overlapping loci of the provided BED +file will be shown as a jitter plot on top of the violin plot.

+
+ +
+

Usage

+ 
plot_gr_violin(
+  gr,
+  columns,
+  highlight = NULL,
+  minoverlap = 0L,
+  highlight_label = NULL,
+  highlight_colors = NULL,
+  remove_top = 0,
+  verbose = TRUE,
+  selection = NULL
+)
+
+ +
+

Arguments

+ + +
gr
+

Scored GRanges object

+ + +
columns
+

Columns in gr to plot

+ + +
highlight
+

BED file to use as highlight for subgroups.

+ + +
minoverlap
+

Minimum overlap required for a bin to be highlighted.

+ + +
highlight_label
+

Label for the highlighted loci set

+ + +
highlight_colors
+

Array of color values for the highlighted groups.

+ + +
remove_top
+

Return range 0-(1-remove_top). By default returns the +whole distribution (remove_top == 0).

+ + +
verbose
+

Put a caption with relevant parameters on the plot.

+ + +
selection
+

A GRanges object to restrict binning to a certain set of +intervals. This is useful for debugging and improving performance of +locus specific analyses.

+ +
+
+

Value

+

A ggplot object.

+
+ +
+ + +
+ + + + + + + diff --git a/reference/tile_seqinfo.html b/reference/tile_seqinfo.html index 308a57b..9eda256 100644 --- a/reference/tile_seqinfo.html +++ b/reference/tile_seqinfo.html @@ -9,7 +9,7 @@ wigglescout - 0.18.1 + 0.19.0