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fix: pep: corrected a few things PEP8-wise
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@afedorov-advestis
afedorov-advestis committed Oct 5, 2023
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286 changes: 144 additions & 142 deletions adrubix/rubixheatmap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -30,11 +30,11 @@ class RubixHeatmap:
Three input files (CSV) or pandas DataFrames (in any combination) are expected:
- Main data (clusterized by applying, for example, NMTF to raw data).
- Main data (clustered by applying, for example, NMTF to raw data).
Example of rows: biomarkers at different timepoints.
Example of columns: patients.
- Metadata for rows. Example: column 1 = timepoint, column 2 = biomarker.
- Metadata for rows. Example: column 1 = time point, column 2 = biomarker.
- Metadata for columns. Example: row 1 = score (Y/N), row 2 = treatment (several options), row 3 = cluster no.
Expand All @@ -60,143 +60,6 @@ class RubixHeatmap:
With `plot_save_path` specified, HTML and PNG are saved according to it,
otherwise, HTML only is saved in current working directory to be able to show the plot.
Parameters
----------
data: Optional[pd.DataFrame]
File with main data
metadata_rows: Optional[pd.DataFrame]
Fle with metadata for row annotations
metadata_cols: Optional[pd.DataFrame]
File with metadata for column annotations
data_path: Optional[str]
Path to a folder with data and metadata
data_file: Optional[str]
Name of the file with main data
metadata_rows_file: Optional[str]
Name of the file with metadata for row annotations
metadata_cols_file: Optional[str]
Name of the file with metadata for column annotations
plot_save_path: Optional[str]
Path to an HTML file for saving the plot. If none is provided, HTML is saved in current working directory
under the name <your_python_script_name>.html and automatically opened in a web browser.
save_html: Union[bool, int, str]
If equal to True / string starting with "T" or "t", e.g. "True" / "1" or 1, save HTML plot
(if save_png is False, will always save HTML)
save_png: Union[bool, int, str]
If equal to True / string starting with "T" or "t", e.g. "True" / "1" or 1,
save a PNG screenshot of HTML plot
png_tool: str
// "native" (default) = with Bokeh's export_png() (requires Selenium + ChromeDriver installed, takes more time)
// "hti" = with html2image library (only requires a Chromium-based browser on the machine,
but leaves transparent background and crops PNG to screen size, thus unreliable for large plots)
color_scaling_quantile: Union[int, float]
Quantile for capping and scaling the data to get rid of outliers (read more about it in the README)
scale_along: Union[int, str, None]
// 0 or "columns" = per columns : x => x / max(column)
// 1 or "rows" = per rows : x => x / max(row)
// None (default, and also any other value except for 0 or 1) = do not scale
normalize_along: Union[int, str, None]
// 0 or "columns" = per columns : x => (x - median(column)) / MAD(column)
// 1 or "rows" = per rows : x => (x - median(row)) / MAD(row)
// None (default, and also any other value except for 0 or 1) = do not normalize
colorbar_title: str
Title of the colorbar for main heatmap
colorbar_height: Optional[int]
Height of the colorbar (default = 1/3 of main heatmap height)
colorbar_location: str
Location of the colorbar: "top", "center" or "bottom" (default), always to the right of the heatmap
show_colorbar: bool
Whether to show the colorbar for main heatmap
show_metadata_rows: bool
Whether to plot row annotations (default True)
show_metadata_rows_labels: bool
Whether to show row annotations' labels along vertical axis (default False)
show_metadata_cols: bool
Whether to plot column annotations (default True)
duplicate_metadata_cols: Optional[bool]
Whether to duplicate column annotations under the main heatmap.
If None, will be set automatically to True for dataframes longer that 70 rows.
show_rows_legend: bool
Whether to plot the legend for row annotations (default True)
rows_legend_onecol: bool
// True (default) = plot row annotations in one column, analogously to column annotations (WIP)
// False = plot row annotations in multiple columns (WIP)
show_cols_legend: bool
Whether to plot the legend for column annotations (default True)
colormap_main: str
Main colormap name, must be known by holoviews (default "coolwarm" / "YlOrRd" for non-negative data).
Ref. 1 https://holoviews.org/user_guide/Colormaps.html#perceptually-uniform-sequential-colormaps
Ref. 2 https://holoviews.org/user_guide/Colormaps.html#diverging-colormaps
nan_color: str
Hex color string "#xxxxxx" or named HTML color for filling NaN values in the main heatmap (default "black")
sep_color: str
Hex color string "#xxxxxx" or named HTML color for filling separators in the main heatmap (default "white")
colormap_metarows: str
Colormap for row annotations, must be known by holoviews (default "Glasbey").
Ref. https://holoviews.org/user_guide/Colormaps.html#categorical-colormaps
colormap_metacols: str
Colormap for column annotations, must be known by holoviews (default "Category20").
Ref. https://holoviews.org/user_guide/Colormaps.html#categorical-colormaps
axes_labels_style: str
Style of row annotations and column annotations names (default "bold", can be "italic")
legend_axes_labels_style: str
Style of legends names (default "italic", can be "bold")
data_columns_label: str
Label to use for main data columns (normally not shown on the plot)
metadata_label: str
Label to use for metadata (default "Metadata")
pixel_size: str
Size of the colorbar "pixel", in screen pixels (default 6)
heatmap_width: Union[int, str, None]
Fixed main plot width in screen pixels (ignores `pixel_size` specified)
// int = in screen pixels
// "proportional" = proportional to fixed main plot height
heatmap_height: Union[int, str, None]
Fixed main plot height in screen pixels (ignores `pixel_size` specified)
// int = in screen pixels
// "proportional" = proportional to fixed main plot width
mrcol_for_legend: Optional[str]
Column of metadata for row annotations to be explained in the legend.
If not specified, the rightmost column is explained.
proper_labels_for_metadata_cols_legend: Optional[dict]
Dict of correspondence between metadata_cols rows' names and names we'd like to show in the legend
(enables to use shorter names for better display)
row_labels_for_highlighting: Optional[list]
Keywords for identifying row labels to be highlighted i.e. specified on the plot (optional)
index_label: Optional[str]
Name of a column in main data DF to set as rows index (optional)
columns_label: Optional[str]
Name of a row in main data DF to set as columns index (optional)
data_rows_to_drop: Optional[list]
Names of rows in main data not intended to be plotted (optional). Nonexistent names will be skipped.
data_cols_to_drop: Optional[list]
Names of columns in main data not intended to be plotted (optional). Nonexistent names will be skipped.
metadata_rows_sep: Optional[str]
Insert row separators in the main DF and the metadata-rows DF before plotting,
according to the specified column (between groups of labels with identical values).
A separator is a row or a group of rows (depending on the DF length and heatmap height)
filled with either minimum value for non-normalized data, or median value for normalized one.
metadata_cols_sep: Optional[str]
Insert column separators in the main DF and the metadata-cols DF before plotting,
according to the specified rows (between groups of labels with identical values).
A separator is a column or a group of columns (depending on the DF length and heatmap height)
filled with either minimum value for non-normalized data, or median value for normalized one.
sep_value: str
// None (default) = separators will be plotted in `sep_color` (default "white")
// "min" = with mininum value of the DF (color will depend on the colormap)
// "median" = with median value of the DF (color will depend on the colormap)
// "adapt" = with mininum value of the DF if data normalisation is not called, median value if called
"""

def __init__(
Expand Down Expand Up @@ -249,6 +112,145 @@ def __init__(
metadata_cols_sep: Optional[str] = None,
sep_value: Optional[str] = None
) -> None:
"""
Parameters
----------
data: Optional[pd.DataFrame]
File with main data
metadata_rows: Optional[pd.DataFrame]
Fle with metadata for row annotations
metadata_cols: Optional[pd.DataFrame]
File with metadata for column annotations
data_path: Optional[str]
Path to a folder with data and metadata
data_file: Optional[str]
Name of the file with main data
metadata_rows_file: Optional[str]
Name of the file with metadata for row annotations
metadata_cols_file: Optional[str]
Name of the file with metadata for column annotations
plot_save_path: Optional[str]
Path to an HTML file for saving the plot. If none is provided, HTML is saved in current working directory
under the name <your_python_script_name>.html and automatically opened in a web browser.
save_html: Union[bool, int, str]
If equal to True / string starting with "T" or "t", e.g. "True" / "1" or 1, save HTML plot
(if save_png is False, will always save HTML)
save_png: Union[bool, int, str]
If equal to True / string starting with "T" or "t", e.g. "True" / "1" or 1,
save a PNG screenshot of HTML plot
png_tool: str
// "native" (default) = with Bokeh's export_png() (requires Selenium + ChromeDriver installed,
takes more time)
// "hti" = with html2image library (only requires a Chromium-based browser on the machine,
but leaves transparent background and crops PNG to screen size, thus unreliable for large plots)
color_scaling_quantile: Union[int, float]
Quantile for capping and scaling the data to get rid of outliers (read more about it in the README)
scale_along: Union[int, str, None]
// 0 or "columns" = per columns : x => x / max(column)
// 1 or "rows" = per rows : x => x / max(row)
// None (default, and also any other value except for 0 or 1) = do not scale
normalize_along: Union[int, str, None]
// 0 or "columns" = per columns : x => (x - median(column)) / MAD(column)
// 1 or "rows" = per rows : x => (x - median(row)) / MAD(row)
// None (default, and also any other value except for 0 or 1) = do not normalize
colorbar_title: str
Title of the colorbar for main heatmap
colorbar_height: Optional[int]
Height of the colorbar (default = 1/3 of main heatmap height)
colorbar_location: str
Location of the colorbar: "top", "center" or "bottom" (default), always to the right of the heatmap
show_colorbar: bool
Whether to show the colorbar for main heatmap
show_metadata_rows: bool
Whether to plot row annotations (default True)
show_metadata_rows_labels: bool
Whether to show row annotations' labels along vertical axis (default False)
show_metadata_cols: bool
Whether to plot column annotations (default True)
duplicate_metadata_cols: Optional[bool]
Whether to duplicate column annotations under the main heatmap.
If None, will be set automatically to True for dataframes longer than 70 rows.
show_rows_legend: bool
Whether to plot the legend for row annotations (default True)
rows_legend_onecol: bool
// True (default) = plot row annotations in one column, analogously to column annotations (WIP)
// False = plot row annotations in multiple columns (WIP)
show_cols_legend: bool
Whether to plot the legend for column annotations (default True)
colormap_main: str
Main colormap name, must be known by holoviews (default "coolwarm" / "YlOrRd" for non-negative data).
Ref. 1 https://holoviews.org/user_guide/Colormaps.html#perceptually-uniform-sequential-colormaps
Ref. 2 https://holoviews.org/user_guide/Colormaps.html#diverging-colormaps
nan_color: str
Hex color string "#xxxxxx" or named HTML color for filling NaN values in the main heatmap (default "black")
sep_color: str
Hex color string "#xxxxxx" or named HTML color for filling separators in the main heatmap (default "white")
colormap_metarows: str
Colormap for row annotations, must be known by holoviews (default "Glasbey").
Ref. https://holoviews.org/user_guide/Colormaps.html#categorical-colormaps
colormap_metacols: str
Colormap for column annotations, must be known by holoviews (default "Category20").
Ref. https://holoviews.org/user_guide/Colormaps.html#categorical-colormaps
axes_labels_style: str
Style of row annotations and column annotations names (default "bold", can be "italic")
legend_axes_labels_style: str
Style of legends names (default "italic", can be "bold")
data_columns_label: str
Label to use for main data columns (normally not shown on the plot)
metadata_label: str
Label to use for metadata (default "Metadata")
pixel_size: str
Size of the colorbar "pixel", in screen pixels (default 6)
heatmap_width: Union[int, str, None]
Fixed main plot width in screen pixels (ignores `pixel_size` specified)
// int = in screen pixels
// "proportional" = proportional to fixed main plot height
heatmap_height: Union[int, str, None]
Fixed main plot height in screen pixels (ignores `pixel_size` specified)
// int = in screen pixels
// "proportional" = proportional to fixed main plot width
mrcol_for_legend: Optional[str]
Column of metadata for row annotations to be explained in the legend.
If not specified, the rightmost column is explained.
proper_labels_for_metadata_cols_legend: Optional[dict]
Dict of correspondence between metadata_cols rows' names and names we'd like to show in the legend
(enables to use shorter names for better display)
row_labels_for_highlighting: Optional[list]
Keywords for identifying row labels to be highlighted i.e. specified on the plot (optional)
index_label: Optional[str]
Name of a column in main data DF to set as rows index (optional)
columns_label: Optional[str]
Name of a row in main data DF to set as columns index (optional)
data_rows_to_drop: Optional[list]
Names of rows in main data not intended to be plotted (optional). Nonexistent names will be skipped.
data_cols_to_drop: Optional[list]
Names of columns in main data not intended to be plotted (optional). Nonexistent names will be skipped.
metadata_rows_sep: Optional[str]
Insert row separators in the main DF and the metadata-rows DF before plotting,
according to the specified column (between groups of labels with identical values).
A separator is a row or a group of rows (depending on the DF length and heatmap height)
filled with either minimum value for non-normalized data, or median value for normalized one.
metadata_cols_sep: Optional[str]
Insert column separators in the main DF and the metadata-cols DF before plotting,
according to the specified rows (between groups of labels with identical values).
A separator is a column or a group of columns (depending on the DF length and heatmap height)
filled with either minimum value for non-normalized data, or median value for normalized one.
sep_value: str
// None (default) = separators will be plotted in `sep_color` (default "white")
// "min" = with minimum value of the DF (color will depend on the colormap)
// "median" = with median value of the DF (color will depend on the colormap)
// "adapt" = with minimum value of the DF if data normalisation is not called, median value if called
"""

# Auxiliary
self.df_titles = ["Data", "Metadata rows", "Metadata cols"]
Expand Down Expand Up @@ -615,7 +617,7 @@ def scale_data(self) -> None:

def cap_scale(x):
quantile = np.percentile(x, quant)
x = x.apply(lambda x: quantile if x > quantile else x)
x = x.apply(lambda y: quantile if y > quantile else y)
x /= quantile
return x

Expand All @@ -635,7 +637,7 @@ def cap_scale(x):
quant_low = 50 - quant / 2
quantile_high = np.percentile(x, quant_high)
quantile_low = np.percentile(x, quant_low)
x = x.apply(lambda x: quantile_high if x > quantile_high else (quantile_low if x < quantile_low else x))
x = x.apply(lambda y: quantile_high if y > quantile_high else (quantile_low if y < quantile_low else y))
x /= quantile_high
return x

Expand All @@ -644,7 +646,7 @@ def center_reduce(x):
dev = x - median
median_abs_dev = np.median(abs(dev))
x = dev / median_abs_dev
x = x.apply(lambda x: 1 if x > 1 else (-1 if x < -1 else x))
x = x.apply(lambda y: 1 if y > 1 else (-1 if y < -1 else y))
return x

self.data = self.data.apply(cap_scale, axis=self.normalize_along)
Expand Down
7 changes: 6 additions & 1 deletion requirements.txt
View file
Original file line number Diff line number Diff line change
@@ -1,3 +1,4 @@
numpy~=1.26.0
pandas~=1.4

bokeh~=2.4
Expand All @@ -10,4 +11,8 @@ selenium~=4.4
chromedriver-binary~=109.0

more-itertools
pytest
pytest~=7.4.2


setuptools~=65.5.1
tomli~=2.0.1

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