Plot imdanovaFilt Object

For plotting an S3 object of type 'imdanovaFilt'

# S3 method for class 'imdanovaFilt'
plot(
  x,
  min_nonmiss_anova = NULL,
  min_nonmiss_gtest = NULL,
  interactive = FALSE,
  x_lab = NULL,
  y_lab = NULL,
  x_lab_size = 11,
  y_lab_size = 11,
  x_lab_angle = 0,
  title_lab = NULL,
  title_lab_size = 14,
  legend_lab = NULL,
  legend_position = "right",
  point_size = 3,
  line_size = 0.75,
  text_size = 3,
  bw_theme = TRUE,
  palette = NULL,
  display_count = TRUE,
  ...
)

Arguments

x

Object of class imdanovaFilt (also a data frame) containing the molecule identifier and number of samples in each group with non-missing values for that molecule

min_nonmiss_anova

An integer indicating the minimum number of non-missing feature values allowed per group for anova_filter. Suggested value is 2.

min_nonmiss_gtest

An integer indicating the minimum number of non-missing feature values allowed per group for gtest_filter. Suggested value is 3.

interactive

logical value. If TRUE produces an interactive plot.

x_lab

character string specifying the x-axis label

y_lab

character string specifying the y-axis label

x_lab_size

integer value indicating the font size for the x-axis. The default is 11.

y_lab_size

integer value indicating the font size for the y-axis. The default is 11.

x_lab_angle

integer value indicating the angle of x-axis labels. The default is 0.

title_lab

character string specifying the plot title.

title_lab_size

integer value indicating the font size of the plot title. The default is 14.

legend_lab

character string specifying the legend title.

legend_position

character string specifying the position of the legend. Can be one of "right", "left", "top", "bottom", or "none". The default is "none".

point_size

integer specifying the size of the points. The default is 3.

line_size

integer specifying the thickness of the line. The default is 0.75.

text_size

integer specifying the size of the text (number of biomolecules per group). The default is 3.

bw_theme

logical value. If TRUE uses the ggplot2 black and white theme.

palette

character string indicating the name of the RColorBrewer palette to use. For a list of available options see the details section in RColorBrewer.

display_count

logical value. Indicates whether the missing value counts by sample will be displayed on the bar plot. The default is TRUE.

...

further arguments passed to or from other methods.

Value

ggplot2 plot object if interactive is FALSE, or plotly plot object if interactive is TRUE

Examples

library(pmartRdata)
data(pep_object)
mypep <- group_designation(omicsData = pep_object, main_effects = "Phenotype")
to_filter <- imdanova_filter(omicsData = mypep)
plot(to_filter, min_nonmiss_anova = 2, min_nonmiss_gtest = 3)