plot_sample_cvheatmap: An experiment to see if I can visualize the genes with the...
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

plot_sample_cvheatmap

R Documentation

An experiment to see if I can visualize the genes with the highest variance.

Description

An experiment to see if I can visualize the genes with the highest variance.

Usage

plot_sample_cvheatmap(
  expt,
  fun = "mean",
  fact = "condition",
  row_label = NA,
  plot_title = NULL,
  Rowv = TRUE,
  Colv = TRUE,
  label_chars = 10,
  dendrogram = "column",
  min_delta = 0.5,
  x_factor = 1,
  y_factor = 2,
  min_cvsd = NULL,
  cv_min = 1,
  cv_max = Inf,
  remove_equal = TRUE
)

Arguments

`expt`	ExpressionSet
`fun`	mean or median
`fact`	Which factor to slice/dice the data?
`row_label`	Label the rows?
`plot_title`	Title for the plot
`Rowv`	Row vs (yeah I forgot what this does.)
`Colv`	Col vs
`label_chars`	Maximum number of characters in the sample IDs.
`dendrogram`	Make a tree of the samples?
`min_delta`	Minimum delta value for filtering
`x_factor`	When plotting two factors against each other, which is x?
`y_factor`	When plotting two factors against each other, which is y?
`min_cvsd`	Include only those with a minimal CV?
`cv_min`	Minimum cv to examine (I think this should be slightly lower)
`cv_max`	Maximum cV to examine (I think this should be limited to ~ 0.7?)
`remove_equal`	Filter uninteresting genes.