plot_df = pd.concat(
[
mofa.factors[[f_x, f_y]],
gexp.loc[["CDH1", "VIM"]].T.add_suffix("_transcriptomics"),
prot.loc[["CDH1", "VIM"]].T.add_suffix("_proteomics"),
ss["Tissue_type"],
],
axis=1,
sort=False,
)
# Tissue plot
ax = GIPlot.gi_tissue_plot(f_x,
f_y,
plot_df,
plot_reg=False,
pal=PALETTE_TTYPE)
ax.set_xlabel(f"Factor {f_x[1:]}")
ax.set_ylabel(f"Factor {f_y[1:]}")
plt.savefig(f"{RPATH}/MultiOmics_{f_x}_{f_y}_tissue_plot.pdf",
bbox_inches="tight")
plt.savefig(f"{RPATH}/MultiOmics_{f_x}_{f_y}_tissue_plot.png",
bbox_inches="tight",
dpi=600)
plt.close("all")
# Continous annotation
for z in ["VIM_proteomics", "CDH1_proteomics"]:
ax = GIPlot.gi_continuous_plot(f_x,
f_y,
p, c, dtype, ctissues = ("UBFD1", "TP63", "crispr", ["Lung"])
plot_df = pd.concat(
[
drespo.loc[[c]].T.add_suffix("_y")
if dtype == "drug" else crispr.loc[[c]].T.add_suffix("_y"),
prot.loc[[p]].T.add_suffix("_prot"),
gexp.loc[[p]].T.add_suffix("_gexp"),
prot_obj.ss["tissue"],
],
axis=1,
sort=False,
).dropna(subset=[f"{c}_y", f"{p}_prot"])
# Protein
ax = GIPlot.gi_tissue_plot(f"{p}_prot", f"{c}_y", plot_df)
if dtype == "drug":
ax.axhline(np.log(drespo_maxc[c]),
ls="--",
lw=.3,
color=CrispyPlot.PAL_DTRACE[1])
ax.set_xlabel(f"{p}\nProtein intensities")
ax.set_ylabel(
f"{c}\n{'Drug response IC50' if dtype == 'drug' else 'CRISPR-Cas9 (log2 FC)'}"
)
plt.savefig(
f"{RPATH}/TopHits_{p}_{c}_{dtype}_regression_tissue_plot.pdf",
bbox_inches="tight",
)
plot_df = pd.concat(
[
drespo.loc[[c]].T.add_suffix("_y")
if dtype == "drug" else crispr.loc[[c]].T.add_suffix("_y"),
prot.loc[[p]].T.add_suffix("_prot"),
gexp.loc[[p]].T.add_suffix("_gexp"),
ss["Tissue_type"],
],
axis=1,
sort=False,
).dropna(subset=[f"{c}_y", f"{p}_prot"])
# Protein
ax = GIPlot.gi_tissue_plot(f"{p}_prot",
f"{c}_y",
plot_df,
pal=PALETTE_TTYPE)
if dtype == "drug":
ax.axhline(np.log(dmaxc[c]),
ls="--",
lw=0.3,
color=CrispyPlot.PAL_DTRACE[1])
ax.set_xlabel(f"{p}\nProtein intensities")
ax.set_ylabel(
f"{c}\n{'Drug response IC50' if dtype == 'drug' else 'CRISPR-Cas9 (log2 FC)'}"
)
plt.savefig(
f"{RPATH}/TopHits_{p}_{c}_{dtype}_regression_tissue_plot.pdf",
bbox_inches="tight",