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params.yml
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binsize: 50000
n_eigs: 128
decomp_mode: "trans"
sample: "THP1"
assembly: "hg38"
n_clusters: [3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20]
#####
# Track configuration
#####
# List of binned quantitative genomic tracks to use for visualization of
# eigenspace and clustering.
# Each track has a type:
# * category: categorical data
# * scalar: quantitative
# * divergent: quantitative, but the default colorscale will be centered at 0.
# Colormapping options for matplotlib/datashader can be specified.
# Each track type has associated default options which can be overridden.
tracks:
# These are some of the default tracks generated during the pipeline.
cluster:
type: "category"
chrom:
type: "category"
GC:
type: "divergent"
options:
cmap: "RdYlBu_r"
vmin: 0.35
vmax: 0.65
centel_abs:
type: "scalar"
options:
cmap: "Greys"
vmin: 0
vmax: 149043529
# Specify additional tracks to be generated from bigwig files.
# Their display options can be customized here.
# Default is to assume type: "scalar".
H3K27ac:
type: "scalar"
# vmin: 0
# vmax: 1.4
H3K27me3:
type: "scalar"
# vmin: 0
# vmax: 0.5
H3K4me3:
type: "scalar"
# vmin: 0
# vmax: 1.5
#####
# Configure which tracks to use in each visualization.
#####
heatmap_groups:
group1:
- centel_abs
- GC
group2:
- H3K27ac
- H3K27me3
- H3K4me3
scatter_groups:
group1:
- cluster
- centel_abs
- GC
- H3K27ac
- H3K27me3
- H3K4me3