Comments (4)
OK, can you also attach the code?
from enrichedheatmap.
Here is the code. Thanks.
`Histone_methylation_HT_Tx_cluster = EnrichedHeatmap(mat_H3K27me3_Tx,
col = col_fun_H3K27me3_Tx,
column_title = "Enrichment of H3K27me3",
column_title_gp = gpar(fontsize = 14),
name = "H3K27me3",
top_annotation = HeatmapAnnotation(enriched = anno_enriched(gp = gpar(col = 1:6, lty = 1:6), yaxis_side = "right", yaxis_facing = "right", yaxis_gp = gpar(fontsize = 10))),
row_title_rot = 0,
top_annotation_height = unit(2, "cm"),
axis_name = c("-2 kb", "TSS", "TTS","+2 kb"),
axis_name_gp = gpar(fontsize = 14),
cluster_rows=TRUE,
km = 6) +
EnrichedHeatmap(mat_H3K4me3_Tx,
col = col_fun_H3K4me3_Tx,
column_title = "Enrichment of H3K4me3",
column_title_gp = gpar(fontsize = 14),
name = "H3K4me3",
top_annotation = HeatmapAnnotation(enriched = anno_enriched(gp = gpar(col = 1:6, lty = 1:6), yaxis_side = "right", yaxis_facing = "right", yaxis_gp = gpar(fontsize = 10))),
row_title_rot = 0,
top_annotation_height = unit(2, "cm"),
axis_name = c("-2 kb", "TSS", "TTS","+2 kb"),
axis_name_gp = gpar(fontsize = 14),
cluster_rows=TRUE,
km = 6) +
EnrichedHeatmap(mat_H3K27ac_Tx,
col = col_fun_H3K27ac_Tx,
column_title = "Enrichment of H3K27ac",
column_title_gp = gpar(fontsize = 14),
name = "H3K27ac",
top_annotation = HeatmapAnnotation(enriched = anno_enriched(gp = gpar(col = 1:6, lty = 1:6), yaxis_side = "right", yaxis_facing = "right", yaxis_gp = gpar(fontsize = 10))),
row_title_rot = 0,
top_annotation_height = unit(2, "cm"),
axis_name = c("-2 kb", "TSS", "TTS","+2 kb"),
axis_name_gp = gpar(fontsize = 14),
cluster_rows=TRUE,
km = 6)+
EnrichedHeatmap(Tx_Bd0d.cpg,
col = methcol,
name = "CpG",
top_annotation = HeatmapAnnotation(enriched = anno_enriched(gp = gpar(col = 2:6, lty = 1:6), yaxis_side = "right", yaxis_facing = "right", yaxis_gp = gpar(fontsize = 10))),
column_title = "CpG",
axis_name = c("-2 kb", "TSS", "TTS","+2 kb"),
axis_name_gp = gpar(fontsize = 14),
cluster_rows=TRUE,
km = 6) +
EnrichedHeatmap(Tx_Bd0d.chg,
col = methcol,
name = "CHG",
top_annotation = HeatmapAnnotation(enriched = anno_enriched(gp = gpar(col = 2:6, lty = 1:6), yaxis_side = "right", yaxis_facing = "right", yaxis_gp = gpar(fontsize = 10))),
column_title = "CHG",
axis_name = c("-2 kb", "TSS", "TTS","+2 kb"),
axis_name_gp = gpar(fontsize = 14),
cluster_rows=TRUE,
km = 6) +
EnrichedHeatmap(Tx_Bd0d.chh,
col = methcol,
name = "CHH",
top_annotation = HeatmapAnnotation(enriched = anno_enriched(gp = gpar(col = 2:6, lty = 1:6), yaxis_side = "right", yaxis_facing = "right", yaxis_gp = gpar(fontsize = 10))),
column_title = "CHH",
axis_name = c("-2 kb", "TSS", "TTS","+2 kb"),
axis_name_gp = gpar(fontsize = 14),
cluster_rows=TRUE,
km = 6)
png("Total_Histone_marks_EnrichedHeatmap_Tx_cluster.png", height =6000, width = 14400, res =600)
draw(Histone_methylation_HT_Tx_cluster, gap = unit(10, "mm"))
dev.off()`
from enrichedheatmap.
In the part where you make methylation heatmap, the setting for color is wrong:
gp = gpar(col = 2:6, ...
it should be
gp = gpar(col = 1:6,
from enrichedheatmap.
oh yes, thanks for pointing the error.
from enrichedheatmap.
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from enrichedheatmap.