plot_ordered_matrix: Plot ordered data matrix
In nlhuong/buds: Bayesian Unidimensional Scaling (BUDS)

Description Usage Arguments Value

Plot a heatmap for a data matrix where columns are reordered according to tau and rows according to either byMean or by maximum value in a window along tau.

1
2
3

plot_ordered_matrix(X, tau, log_trans = FALSE, norm_samples = FALSE,
  keep_features = NULL, nfeatures = 500, byMean = TRUE, window = 5,
  minsum = 0)

`X`	A data frame of matrix where rows are features and columns are samples.
`tau`	A vector with latent 1D coordinates for data points.
`log_trans`	[Optional] A boolean for whether to log transform the data before plotting. Default is FALSE.
`norm_samples`	A boolean whether the columns (samples) should be normalize to even total sum.
`keep_features`	[Optional] A list of features (rows) that must be included in the heatmap.
`nfeatures`	The number of features to keep. Default is 500.
`byMean`	A boolean whether to order features by their "mean tau" value. If FALSE the features are ordered by maximum in a window along tau.
`window`	An integer for the window size. Default is 5.
`minsum`	A for the minimum sum for a feature in a data matrix.