rank_count_plot: Rank-Count plot
In jmw86069/salsa: Single-cell Amalgamation by Latent Semantic Analysis (SALSA)

Description Usage Arguments Details Value See Also Examples

Rank-Count plot

1 2	rank_count_plot(x, log = c("x", "y"), flip_axes = FALSE, highlight_range = NULL, ...)

`x`	numeric or integer vector of counts
`log`	character vector indicating the axis or axes log-transform, with any presence of `"x"` and `"y"`.
`flip_axes`	logical indicating whether to flip the x- and y-axis coordinates.
`highlight_range`	optional numeric range to highlight, intended to represent the range of counts selected for downstream analysis.
`...`	additional arguments are ignored

This function creates a classic "knee plot" showing "Rank" on the x-axis, and "Count" on the y-axis, typically with log-scaled x- and y-axes.

ggplot object sufficient to plot the Rank-Count data, including the optional highlighted points based upon the highlight_range values.

Other SALSA visualization functions: plot_fr_wei

library(salsa);
data(oz2_numi_per_cell);

usecounts <- sort(oz2_numi_per_cell$count);

rank_count_plot(usecounts,
   highlight_range=c(100,2500)) +
   ggtitle("All counts unfiltered");

# after filtering, it may help add y=1 to the axis range
usecounts <- usecounts[usecounts >= 16];
rank_count_plot(usecounts,
   highlight_range=c(100,2500)) +
   expand_limits(y=c(1,NA)) +
   ggtitle("Filtered for counts >= 16");