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

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.

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.

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.

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).

Examples

Run this code

# NOT RUN {
immdata.top <- top.cross(immdata)
top.cross.plot(immdata.top)
# }