top.cross: Perform sequential cross starting from the top of a data...

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

Description

top.cross - get top crosses of the given type between each pair of the given data.frames with top.cross function.

top.cross.vec - get vector of cross values for each top with the top.cross.vec function.

top.cross.plot - plot a plots with result with the top.cross.plot function.

Usage

top.cross(.data, .n = NA, .data2 = NULL, .type = 'ave', .norm = F, .verbose = T)

top.cross.vec(.top.cross.res, .i, .j)

top.cross.plot(.top.cross.res, .xlab = 'Top X clonotypes', 
               .ylab = 'Normalised number of shared clonotypes', .nrow = 2,
               .legend.ncol = 1, .logx = T, .logy = T)

Arguments

.data	Either list of data.frames or a data.frame.
.n	Integer vector of parameter appled to the head function; same as .n in the top.fun function. See "Details" for more information.
.data2	Second data.frame or NULL if .data is a list.
.type	Parameter .type to the tcR::intersect function.
.norm	Parameter .norm to the tcR::intersect function.
.verbose	if T then plot a progress bar.
.top.cross.res	Result from the top.cross function.
.i, .j	Coordinate of a cell in each matrix.
.xlab	Name for a x-lab.
.ylab	Name for a y-lab.
.nrow	Number of rows of sub-plots in the output plot.
.legend.ncol	Number of columns in the output legend.
.logx	if T then transform x-axis to log-scale.
.logy	if T then transform y-axis to log-scale.

Details

Parameter .n can have two possible values. It could be either integer vector of numbers (same as in the top.fun function) or NA and then it will be replaced internally by the value .n <- seq(5000, min(sapply(.data, nrow)), 5000).

Value

top.cross - return list for each element in .n with intersection matrix (from tcR::intersectClonesets).

top.cross.vec - vector of length .n with .i:.j elements of each matrix.

top.cross.plot - grid / ggplot object.

See Also

intersect

Examples

## Not run: 
immdata.top <- top.cross(immdata)
top.cross.plot(immdata.top)

## End(Not run)

tcR documentation built on July 2, 2020, 3:18 a.m.