Description Usage Arguments Details Value Examples
Heatmap of specified tidy metagene tbl.
1 |
tbl |
tidy metagene tbl |
color_by |
name of column from tbl to use as value (default='value') |
do_interpolate |
interpolate geom_raster output (default=FALSE) |
uses ggplot2 to create plot of the heatmap
ggplot2 object
1 2 3 4 5 6 7 8 9 10 11 | bedfile <- system.file("extdata", "Chen_PROMPT_TSSs_liftedTohg38.bed", package = "RMetaTools")
bw_plus <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_plus_hg38.bw", package = "RMetaTools")
bw_minus <- system.file("extdata", "GSM1573841_mNET_8WG16_siLuc_minus_hg38.bw", package = "RMetaTools")
anno=bedfile;anchor='center';upstream=1000;downstream=1000;window_size=10
collapse_fun = rowMeans;negate_neg_strand_values=FALSE
metamat <- metagene_matrix(bw_plus, bw_minus, bedfile, anchor, upstream, downstream, window_size)
plot_htmp(metamat, color_by='value', do_interpolate=FALSE)
#log2 values incl pseudocount
metamat %<>% mutate(log2_value = log2(value+1))
plot_htmp(metamat, color_by='log2_value', do_interpolate=FALSE)
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