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Running MARK02 - Rerun Post-Log-Prob Fix #158

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Running MARK02 - Rerun Post-Log-Prob Fix #158

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15576f4
setup mark02 for rerun
gordonkoehn Aug 29, 2023
b0373f7
fix paths
gordonkoehn Aug 29, 2023
76e358c
untested legend outside of plot
gordonkoehn Aug 30, 2023
5dbf40c
merged plot changes in
gordonkoehn Aug 30, 2023
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8 changes: 4 additions & 4 deletions workflows/mark02.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,7 @@ CS_seed = 42 # <-- configure cell simulation seed here
#####################
# True Tree Parameters
tree_types = ["r"] # <-- configure tree type here ["r","s","d"]
tree_seeds = [42]#, 34] # <-- configure tree seed here
tree_seeds = [42, 34] # <-- configure tree seed here

#####################
#####################
Expand Down Expand Up @@ -242,17 +242,17 @@ rule combined_chain_histogram:
sublist = [float(x) for x in sublist]

# Create histogram for the sublist with the color and label
ax.hist(sublist,bins='auto', range = (0,1),alpha=0.5,color=colors[color_index],label=labels[i])
ax.hist(sublist, bins='auto', range = (0,1),alpha=0.5,color=colors[color_index],label=labels[i])

# Set labels and title
ax.set_xlabel(f"Similarity: {wildcards.metric}")
ax.set_ylabel('Frequency')

# Add a legend
ax.legend()
ax.legend(bbox_to_anchor = (1.04, 0.5), loc = "center left", borderaxespad = 0)

# save the histogram
fig.savefig(Path(output.combined_chain_histogram))
fig.savefig(Path(output.combined_chain_histogram), bbox_inches="tight")



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5 changes: 2 additions & 3 deletions workflows/tree_inference.smk
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Expand Up @@ -19,9 +19,8 @@ from pyggdrasil.tree_inference import (
###############################################
## Relative path from DATADIR to the repo root

#REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil"
REPODIR = ".."
#DATADIR = "/cluster/work/bewi/members/gkoehn/data"
REPODIR = "/cluster/work/bewi/members/gkoehn/repos/PYggdrasil"
DATADIR = "/cluster/work/bewi/members/gkoehn/data"

###############################################

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