extract_syndromic_plot: Extract the syndromic plot

In ucsf-ferguson-lab/syndRomics: Component loading interpretation and visualization with syndromic plots

Extract the syndromic plot

Description

Extract the syndromic plot of a given list of loadings and specified pc.

Usage

extract_syndromic_plot(
  load_df,
  pc,
  cutoff = 0.5,
  VAF,
  arrow_size_multi = 10,
  repel = F,
  plot_legend = TRUE,
  plot_cutoff = TRUE,
  text_size = 6,
  var_order = "abs decreasing",
  colors = c("steelblue1", "white", "firebrick1")
)

Arguments

load_df	data.frame with the loadings. Format: one column named Variable and a column for each PC. It can be extracted from a prcomp or princals object using stand_loadings().
pc	String. Name of the PC in load_df to plot.
cutoff	Numeric. Value of the loadings threshold (i.e. |loadings| > cutoff) to plot. Default = 0.5
VAF	String. Text for the center of the syndromic plot. The text generally corresponds to the variance accounted for (VAF) of the PC. If pca is the results of prcomp or princals, VAF is internally calculated.
arrow_size_multi	Numeric. Controls the size of the arrows proportional to the loading. Default=10
repel	Logical. Whether to repel the text for preventing text overlap. Default=FALSE
plot_legend	Logical. Whether to plot the legend or not. Default=TRUE
plot_cutoff	Logical. Whether to report the cutoff on the legend or not. Default = TRUE
text_size	Numeric. Controls for the size of the text. Default=9.
var_order	Character, character vector or numeric vector. Specify the order of the variables in the plot by the loading values, starting at 12 o’clock and moving counterclockwise. Possible values: 'abs decreasing': plot by decreasing absolute value; 'abs increasing': plot by increasing absolute value; 'decreasing'; or 'increasing’. A vector can be specified with a custom order of the variables to plot. If a numeric vector is provided, the variables will be ordered as specified by the numbers. If a character vector is provided, the variables will be ordered in the same order as the variable names provided. In case of vector, non-specified variables will be excluded from the plot.
colors	Character vector of length 3. Vector with the character name or hexadecimal number (e.g. "#FF0000") of three colors, the lower color, the middle color and the higher color for the gradient used in the plot. Hexadecimal number can be obtained using rgb for example.

Value

A ggplot2 object of the syndromic plot.

Author(s)

Abel Torres Espin

ucsf-ferguson-lab/syndRomics documentation built on June 26, 2022, 5:36 p.m.