sigminer (version 1.0.6)

show_sig_number_survey: Show Simplified Signature Number Survey

Description

sig_estimate shows comprehensive rank survey generated by NMF package, sometimes it is hard to consider all measures. Here provides a one or two y-axis visualization method to help users determine the optimal signature number (showing both stability ("cophenetic") and error (RSS) at default). Users can also set custom measures to show.

Usage

show_sig_number_survey(
  object,
  x = "rank",
  left_y = "cophenetic",
  right_y = "rss",
  left_name = left_y,
  right_name = toupper(right_y),
  left_color = "black",
  right_color = "red"
)

Arguments

object

a Survey object generated from sig_estimate, or a data.frame contains at least rank columns and columns for one measure.

x

column name for x axis.

left_y

column name for left y axis.

right_y

column name for right y axis.

left_name

label name for left y axis.

right_name

label name for right y axis.

left_color

color for left axis.

right_color

color for right axis.

Value

a ggplot object

See Also

sig_estimate for estimating signature number for sig_extract, show_sig_number_survey2 for more visualization method.

Examples

# NOT RUN {
load(system.file("extdata", "toy_copynumber_tally_M.RData",
  package = "sigminer", mustWork = TRUE
))
library(NMF)
cn_estimate <- sig_estimate(cn_tally_M$nmf_matrix,
  cores = 1, nrun = 5,
  verbose = TRUE
)

# Show two measures
show_sig_number_survey(cn_estimate)
# Show one measure
p <- show_sig_number_survey(cn_estimate, right_y = NULL)
p
p <- add_h_arrow(p, x = 4.1, y = 0.953, label = "selected number")
p

# Show data from a data.frame
show_sig_number_survey(cn_estimate$survey)
# Show other measures
head(cn_estimate$survey)
show_sig_number_survey(cn_estimate$survey,
  right_y = "dispersion",
  right_name = "dispersion"
)
show_sig_number_survey(cn_estimate$survey,
  right_y = "evar",
  right_name = "evar"
)
# }