Plot a heatmap of average methylation clustering
gpatterns.plot_clustering(avgs, rows_clust_method = "kmeans", K = NULL,
cluster_cols = TRUE, show_row_clust = TRUE, annotation = NULL,
annotation_colors = NULL, annotation_col = NULL, show_rownames = FALSE,
show_colnames = FALSE, cluster_gaps = FALSE, color_pal = .blue_red_pal,
fontsize = 8, fontsize_row = fontsize, fontsize_col = fontsize,
main = NULL, device = "png", fig_ofn = NULL, width = 2100,
height = 2000, res = 300, plot = TRUE, motif_enrich = NULL,
cluster_motifs = TRUE, qval_thresh = 0.05, show_sig = TRUE,
motif_fontsize_col = fontsize * 0.8, motif_fontsize_sig = fontsize * 1.3,
...)
Arguments
- avgs
- output of gpatterns.cluster_avg_meth
- cluster_cols
- boolean values determining if columns should be clustered or
hclust object.
- annotation
- deprecated parameter that currently sets the annotation_col if it is missing
- annotation_colors
- list for specifying annotation_row and
annotation_col track colors manually. It is possible to define the colors
for only some of the features. Check examples for details.
- annotation_col
- similar to annotation_row, but for columns.
- show_rownames
- boolean specifying if column names are be shown.
- show_colnames
- boolean specifying if column names are be shown.
- fontsize
- base fontsize for the plot
- fontsize_row
- fontsize for rownames (Default: fontsize)
- fontsize_col
- fontsize for colnames (Default: fontsize)
- main
- the title of the plot
- fig_ofn
- output filename of the figure. if NULL would plot to current device
- width
- width ('png' parameter)
- height
- height ('png' parameter)
- plot
- if FALSE, would only return the clustering
- ...
- other pheatmap1 parameters