explore_logratios {coda4microbiome}

explore_logratios

Description

Explores the association of each log-ratio with the outcome. Summarizes the importance of each variable (taxa) as the aggregation of the association measures of those log-ratios involving the variable. The output includes a plot of the association of the log-ratio with the outcome where the variables (taxa) are ranked by importance

Usage

explore_logratios(
  x,
  y,
  decreasing = TRUE,
  measure = "AUC",
  covar = NULL,
  shownames = FALSE,
  maxrow = 15,
  maxcol = 15,
  showtitle = TRUE,
  mar = c(0, 0, 1, 0)
)

Arguments

x

abundance matrix or data frame (rows are samples, columns are variables (taxa))

y

outcome (binary or continuous); data type: numeric, character or factor vector

decreasing

order of importance (default = TRUE)

measure

association measures "AUC", "Pearson","Spearman", "glm" (default = "AUC")

covar

data frame with covariates (default = NULL)

shownames

logical, if TRUE, shows the names of the variables in the rows of the plot (default = FALSE)

maxrow

maximum number of rows to display in the plot (default = 15)

maxcol

maximum number of columns to display in the plot (default = 15)

showtitle

logical, if TRUE, shows the title of the plot (default = TRUE)

mar

mar numerical vector of the form c(bottom, left, top, right) which gives the number of lines of margin to be specified on the four sides of the plot (default mar=c(0,0,1,0))

Value

list with "max log-ratio","names max log-ratio", "order of importance", "name of most important variables", "association log-ratio with y" and "top log-ratios plot"

Author(s)

M. Calle - T. Susin

Examples

data(HIV, package = "coda4microbiome")

explore_logratios(x_HIV,y_HIV)