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cos model with transcript feats #161

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151 changes: 151 additions & 0 deletions fish_morphology_code/analysis/notebook_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,38 @@
"Peak distance (μm)",
]

BAR_PLOT_COLUMNS_myh67_13 = [
"Cell area (μm^2)",
"Cell aspect ratio",
"Fraction cell area background",
"Fraction cell area diffuse/other",
"Fraction cell area fibers",
"Fraction cell area disorganized puncta",
"Fraction cell area organized puncta",
"Fraction cell area organized z-disks",
"Max coefficient var",
"Peak height",
"Peak distance (μm)",
"MYH7 (count/μm^2)",
"MYH6 (count/μm^2)",
]

BAR_PLOT_COLUMNS_myh67_11 = [
"Cell area (μm^2)",
"Cell aspect ratio",
"Fraction cell area background",
"Fraction cell area diffuse/other",
"Fraction cell area fibers",
"Fraction cell area disorganized puncta",
"Fraction cell area organized puncta",
"Fraction cell area organized z-disks",
"Max coefficient var",
"Peak height",
"Peak distance (μm)",
]

BAR_PLOT_COLUMNS_myh67_2 = ["MYH7 (count/μm^2)", "MYH6 (count/μm^2)"]

SHORT_FEAT_NAME_MAP = {
c: c.replace("Fraction cell area", "")
.replace("(μm^2)", "")
Expand All @@ -51,7 +83,39 @@
for c in BAR_PLOT_COLUMNS
}

SHORT_FEAT_NAME_MAP_11 = {
c: c.replace("Fraction cell area", "")
.replace("(μm^2)", "")
.replace("(μm)", "")
.replace("(count/μm^2)", "")
.strip()
.capitalize()
for c in BAR_PLOT_COLUMNS
}

SHORT_FEAT_NAME_MAP_13 = {
c: c.replace("Fraction cell area", "")
.replace("(μm^2)", "")
.replace("(μm)", "")
.replace("(count/μm^2)", "")
.strip()
.capitalize()
for c in BAR_PLOT_COLUMNS_myh67_13
}

SHORT_FEAT_NAME_MAP_2 = {
c: c.replace("Fraction cell area", "")
.replace("(μm^2)", "")
.replace("(μm)", "")
.replace("(count/μm^2)", "")
.strip()
.capitalize()
for c in BAR_PLOT_COLUMNS_myh67_2
}

BAR_PLOT_COLUMNS_SHORT = [SHORT_FEAT_NAME_MAP[v] for v in BAR_PLOT_COLUMNS]
BAR_PLOT_COLUMNS_SHORT_13 = BAR_PLOT_COLUMNS_SHORT + ["Myh7", "Myh6"]
BAR_PLOT_COLUMNS_SHORT_2 = ["Myh7", "Myh6"]

PROBE_ORDER = ["MYH6", "MYH7", "COL2A1", "H19", "TCAP", "ATP2A2", "BAG3", "HPRT1"]

Expand Down Expand Up @@ -118,6 +182,41 @@ def boot_regression(
"Peak distance (μm)": "Global alignment",
}

FEATURE_TYPE_MAP_myh67_13 = {
"Cell area (μm^2)": "Cell features",
"Cell aspect ratio": "Cell features",
"Fraction cell area background": "Local organization",
"Fraction cell area diffuse/other": "Local organization",
"Fraction cell area fibers": "Local organization",
"Fraction cell area disorganized puncta": "Local organization",
"Fraction cell area organized puncta": "Local organization",
"Fraction cell area organized z-disks": "Local organization",
"Max coefficient var": "Global alignment",
"Peak height": "Global alignment",
"Peak distance (μm)": "Global alignment",
"MYH7 (count/μm^2)": "Transcript",
"MYH6 (count/μm^2)": "Transcript",
}

FEATURE_TYPE_MAP_myh67_11 = {
"Cell area (μm^2)": "Cell features",
"Cell aspect ratio": "Cell features",
"Fraction cell area background": "Local organization",
"Fraction cell area diffuse/other": "Local organization",
"Fraction cell area fibers": "Local organization",
"Fraction cell area disorganized puncta": "Local organization",
"Fraction cell area organized puncta": "Local organization",
"Fraction cell area organized z-disks": "Local organization",
"Max coefficient var": "Global alignment",
"Peak height": "Global alignment",
"Peak distance (μm)": "Global alignment",
}

FEATURE_TYPE_MAP_myh67_2 = {
"MYH7 (count/μm^2)": "Transcript",
"MYH6 (count/μm^2)": "Transcript",
}


def ci_low(x, ci_extent=CI_EXTENT):
return x.quantile((1 - ci_extent) / 2)
Expand Down Expand Up @@ -205,6 +304,58 @@ def make_regression_bar_plot(
return fig, ax


def make_regression_bar_plot_more_feats(
df_in,
dims=(4, 3),
x="Feature",
order=BAR_PLOT_COLUMNS_SHORT,
y="Feature weight (mean)",
hue="Feature Type",
palette=sns.color_palette("husl", 3),
ecolor="k",
elinewidth=1,
capsize=4,
ylabel="Feature weight in linear model\n(regression coefficient)",
title="",
short_names=SHORT_FEAT_NAME_MAP,
):
"""standardized bar plots of coefficients + error bars from bootstrapped regression"""
df = df_in.copy()
df["Feature"] = df["Feature"].map(short_names)

fig, ax = plt.subplots(figsize=dims)
feat_chart = sns.barplot(
data=df, x=x, order=order, y=y, hue=hue, palette=palette, dodge=False
)

err = np.array(
(
(df["Feature weight (mean)"] - df["Feature weight (CI low)"]).values,
(df["Feature weight (CI high)"] - df["Feature weight (mean)"]).values,
)
)

plt.errorbar(
x=df.set_index("Feature").loc[order, :].reset_index()["Feature"],
y=df.set_index("Feature").loc[order, :].reset_index()["Feature weight (mean)"],
fmt="none",
yerr=err,
ecolor=ecolor,
elinewidth=elinewidth,
capsize=capsize,
)

ax.set_title(title.replace("_", " "))

sns.despine()

feat_chart.set_xticklabels(
feat_chart.get_xticklabels(), rotation=45, horizontalalignment="right"
)
feat_chart.set(ylabel=ylabel)
plt.legend(bbox_to_anchor=(1.0, 0.7), frameon=False)


def get_pred_true(
df,
X_cols=BAR_PLOT_COLUMNS,
Expand Down