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Added rothman and dropped panel amplified samples
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@simonleandergrimm
simonleandergrimm committed May 28, 2024
1 parent a9fa925 commit 6ffee77
Showing 1 changed file with 73 additions and 21 deletions.
94 changes: 73 additions & 21 deletions figures/composite_fig_1.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@
"Yang 2020": ["PRJNA645711"],
"Spurbeck 2023": ["PRJNA924011"],
"CC 2021": ["PRJNA661613"],
# "Rothman 2021": ["PRJNA729801"], # not yet run through the pipeline
"Rothman 2021": ["PRJNA729801"], # not yet run through the pipeline
}
#
# "Bengtsson-Palme 2016": {
Expand Down Expand Up @@ -169,6 +169,7 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:
fine_taxonomy = pd.read_csv(
f"../taxonomy/{study_bioproject}/kraken_reports.tsv", sep="\t"
)

fine_taxonomy_dfs = {
sample: df for sample, df in fine_taxonomy.groupby("sample")
}
Expand All @@ -186,6 +187,7 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:
)

samples = metadata_samples.keys()
modified_study = study

if study == "Bengtsson-Palme 2016":
samples = [
Expand All @@ -195,6 +197,7 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:
"Inlet"
)
]
modified_study = "Bengtsson-\nPalme 2016"

if study == "Ng 2019":
samples = [
Expand All @@ -205,7 +208,23 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:

for sample in samples:

if metadata_samples[sample].get("enrichment") == "panel":
if study == "Brumfield 2022":
if metadata_samples[sample].get("na_type") == "RNA":
print("brumfield is rna")
modified_study = "Brumfield 2022\n(RNA Subset)"
elif metadata_samples[sample].get("na_type") == "DNA":
print("brumfield is dna")
modified_study = "Brumfield 2022\n(DNA Subset)"

# print(metadata_samples[sample])
# print(
# metadata_samples[sample].get("enrichment"), study, sample
# )
if (
metadata_samples[sample].get("enrichment") == "enriched"
or metadata_samples[sample].get("enrichment") == "1"
):
print(f"{sample} from study {modified_study} is panel")
continue

total_reads = sample_read_pairs[sample]
Expand All @@ -232,7 +251,11 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:
)

hv_family_data.append(
{"study": study, "sample": sample, **hv_family_counts_dict}
{
"study": modified_study,
"sample": sample,
**hv_family_counts_dict,
}
)

sample_fine_taxonomy = fine_taxonomy_dfs[sample]
Expand Down Expand Up @@ -260,7 +283,7 @@ def assemble_plotting_dfs() -> tuple[pd.DataFrame, pd.DataFrame]:

viral_composition_data.append(
{
"study": study,
"study": modified_study,
"sample": sample,
"Human-Infecting Viruses": hv_relative_abundance,
**taxa_abundances,
Expand Down Expand Up @@ -300,6 +323,7 @@ def shape_hv_family_df(hv_family_df: pd.DataFrame) -> pd.DataFrame:


def shape_vir_comp_df(viral_composition_df: pd.DataFrame) -> pd.DataFrame:
print(viral_composition_df["study"].unique())

viral_composition_df = viral_composition_df.melt(
id_vars=["study", "sample"],
Expand Down Expand Up @@ -333,7 +357,7 @@ def order_df(
key=lambda col: col.map({k: i for i, k in enumerate(na_type_order)}),
)

df["study"] = df["study"].str.replace("-", "-\n")
# df["study"] = df["study"].str.replace("-", "-\n")

return df

Expand Down Expand Up @@ -363,9 +387,9 @@ def boxplot(
"Brinch 2020",
"Ng 2019",
"Maritz 2019",
"Brumfield 2022",
# "Brumfield 2022\n(RNA Subset)",
# "Rothman 2021",
"Brumfield 2022\n(DNA Subset)",
"Brumfield 2022\n(RNA Subset)",
"Rothman 2021",
"Yang 2020",
"Spurbeck 2023",
"CC 2021",
Expand Down Expand Up @@ -433,14 +457,22 @@ def boxplot(

def get_study_nucleic_acid_mapping() -> dict[str, str]:
study_nucleic_acid_mapping = {
study: metadata["na_type"]
for study, metadata in metadata_papers.items()
"Bengtsson-\nPalme 2016": "DNA",
"Munk 2022": "DNA",
"Brinch 2020": "DNA",
"Ng 2019": "DNA",
"Maritz 2019": "DNA",
"Brumfield 2022": "DNA + RNA",
"Rothman 2021": "RNA",
"Yang 2020": "RNA",
"Spurbeck 2023": "RNA",
"CC 2021": "RNA",
}

# if "Brumfield 2022" in study_nucleic_acid_mapping:
# study_nucleic_acid_mapping["Brumfield 2022\n(DNA Subset)"] = "DNA"
# study_nucleic_acid_mapping["Brumfield 2022\n(RNA Subset)"] = "RNA"
# del study_nucleic_acid_mapping["Brumfield 2022"]
if "Brumfield 2022" in study_nucleic_acid_mapping:
study_nucleic_acid_mapping["Brumfield 2022\n(DNA Subset)"] = "DNA"
study_nucleic_acid_mapping["Brumfield 2022\n(RNA Subset)"] = "RNA"
del study_nucleic_acid_mapping["Brumfield 2022"]
return study_nucleic_acid_mapping


Expand All @@ -449,15 +481,19 @@ def return_study_order(viral_composition_df: pd.DataFrame) -> list[str]:
viral_composition_df["na_type"] = viral_composition_df["study"].map(
study_nucleic_acid_mapping
)
order = (
viral_composition_df[viral_composition_df["na_type"] == "DNA"][
"study"
].unique()
study_order = (
viral_composition_df[viral_composition_df["na_type"] == "DNA"]["study"]
.unique()
.tolist()
+ viral_composition_df[viral_composition_df["na_type"] == "RNA"][
"study"
].unique()
]
.unique()
.tolist()
)

return study_order


def barplot(
ax: plt.Axes, hv_family_df: pd.DataFrame, study_order: list
Expand All @@ -475,9 +511,25 @@ def barplot(
"#d9d9d9",
]

order = [
"Bengtsson-\nPalme 2016",
"Munk 2022",
"Brinch 2020",
"Ng 2019",
"Maritz 2019",
"Brumfield 2022\n(DNA Subset)",
"Brumfield 2022\n(RNA Subset)",
"Rothman 2021",
"Yang 2020",
"Spurbeck 2023",
"CC 2021",
]

hv_family_df.set_index("study", inplace=True)
print(hv_family_df)
print(order)

hv_family_df.loc[study_order].plot(
hv_family_df.loc[order].plot(
kind="barh",
stacked=True,
color=ten_color_palette,
Expand Down Expand Up @@ -559,7 +611,7 @@ def start():
viral_composition_df,
)

study_order = [text.get_text() for text in boxplot_ax.get_yticklabels()]
study_order = return_study_order(viral_composition_df)

barplot(fig.add_subplot(gs[1, :]), hv_family_df, study_order)
##
Expand Down

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