autoplot.biclustermd {biclustermd} | R Documentation |
Make a heatmap of sparse biclustering results
Description
Make a heatmap of sparse biclustering results
Usage
## S3 method for class 'biclustermd'
autoplot(
object,
axis.text = NULL,
reorder = FALSE,
transform_colors = FALSE,
c = 1/6,
cell_alpha = 1/5,
col_clusts = NULL,
row_clusts = NULL,
...
)
Arguments
object |
An object of class "biclustermd". |
axis.text |
A character vector specifying for which axes text should be
drawn. Can be any of |
reorder |
A logical. If |
transform_colors |
If equals |
c |
Value to scale the data by before running it through a standard normal CDF. Default is 1/6. |
cell_alpha |
A scalar defining the transparency of shading over a cell and by default this equals 1/5. The color corresponds to the cell mean. |
col_clusts |
A vector of column cluster indices to display. If |
row_clusts |
A vector of row cluster indices to display. If |
... |
Arguments to be passed to |
Value
An object of class ggplot.
Examples
data("synthetic")
bc <- biclustermd(synthetic, col_clusters = 3, row_clusters = 2,
miss_val = mean(synthetic, na.rm = TRUE),
miss_val_sd = sd(synthetic, na.rm = TRUE),
col_min_num = 2, row_min_num = 2,
col_num_to_move = 1, row_num_to_move = 1,
max.iter = 10)
bc
autoplot(bc)
autoplot(bc, axis.text = c('x', 'row')) +
ggplot2::scale_fill_distiller(palette = "Spectral", na.value = "white")
# Complete shading
autoplot(bc, axis.text = c('col', 'row'), cell_alpha = 1)
# Transformed values and no shading
autoplot(bc, transform_colors = TRUE, c = 1/20, cell_alpha = 0)
# Focus on row cluster 1 and column cluster 2
autoplot(bc, col_clusts = 2, row_clusts = 1)