pheatmap API

pheatmap.pheatmap(mat: DataFrame, cmap: Union[str, Colormap, list] = 'bwr', vmin: Optional[float] = None, vmax: Optional[float] = None, name: Optional[str] = None, rownames: Optional[ndarray] = None, colnames: Optional[ndarray] = None, rownames_side: str = 'left', colnames_side: str = 'bottom', show_rownames: bool = True, show_colnames: bool = True, rownames_style: dict = {'rotation': 0, 'size': 6}, colnames_style: dict = {'rotation': 0, 'size': 6}, edgecolor: str = 'none', edgewidth: float = 1, annotation_row: Optional[DataFrame] = None, annotation_col: Optional[DataFrame] = None, annotation_row_cmaps: Optional[Dict[str, Union[str, Colormap, list]]] = None, annotation_col_cmaps: Optional[Dict[str, Union[str, Colormap, list]]] = None, show_annotation_row_names: bool = True, show_annotation_col_names: bool = True, legend_tick_locs: Optional[Dict[str, Sequence]] = None, legend_tick_labels: Optional[Dict[str, Sequence]] = None, legend_tick_labels_styles: Dict = {'size': 6}, legend_titles: Optional[Dict[str, bool]] = None, legend_title_styles: Dict = {'size': 6}, width: float = 8, height: float = 6, wspace: float = 0.1, hspace: float = 0.1, annotation_bar_width: float = 0.03, legend_bar_width: float = 0.045, annotation_bar_space: float = 0.2, legend_bar_space: float = 1) → Figure

Plot heatmap with annotation bars

matDataFrame

the main heatmap DataFrame

cmapUnion[str, Colormap, list], optional

the colormap of heatmap, by default “bwr”

vminfloat, optional

the minemum value scaled. by default None, use the minemum value of mat

vmaxfloat, optional

the maximum value scaled. by default None, use the maximum value of mat

namestr, optional

the name of heatmap, by default None, use “heatmap” as the name of heatmap

rownamesndarray, optional

the row names provided, by default None, use the row names of main heatmap DataFrame

colnamesndarray, optional

the column names provided, by default None, use the column names of main heatmap DataFrame

rownames_sidestr, optional

show row names on which side(“left” or “right”)? by default “left”

colnames_sidestr, optional

show column names on which side(“top” or “bottom”)? by default “bottom”

show_rownamesbool, optional

whether show row names? by default True

show_colnamesbool, optional

whether show column names? by default True

rownames_styledict, optional

modify row names’ style, such as, fontsize, fontstyle, etc. See more information on [matplotlib.text.Text](https://matplotlib.org/stable/api/text_api.html#matplotlib.text.Text). by default dict(rotation=0, size=6)

colnames_styledict, optional

see rownames_style, by default dict(rotation=0, size=6)

edgecolorstr, optional

the color of heatmap’s cell edge, by default “none”, no edge. !Note: If provide None, will use the rcParams[“patch.edgecolor”], it default as “black”.

edgewidthfloat, optional

the width of heatmap’s cell edge, by default 1

annotation_rowDataFrame, optional

DataFrame used to create row Annotationbar, by default None

annotation_colDataFrame, optional

DataFrame used to create column Annotationbar, by default None

annotation_row_cmapsDict[str, Union[str, Colormap, list]], optional

Colormaps for each Annotationbar, keys are the DataFrame’s columns, by default None, use “viridis” for continuous and “tab20” for discrete

annotation_col_cmapsDict[str, Union[str, Colormap, list]], optional

see annotation_row_cmaps, by default None

show_annotation_row_namesbool, optional

whether show row Annotationbar’s name, by default True

show_annotation_col_namesbool, optional

whether show column Annotationbar’s name, by default True

legend_tick_locsDict[str, Sequence], optional

modify the tick locations of legend, keys are the name of heatmap or the column names of annotation DataFrame, by default None

legend_tick_labelsDict[str, Sequence], optional

modify the tick labels of legend, keys are the name of heatmap or the column names of annotation DataFrame. The length of each legend tick labels must be matched with its tick locations. by default None

legend_tick_labels_stylesDict, optional

modify the each legend tick labels’ style. Keys are the name of heatmap or the column names of annotation DataFrame. More informations see rownames_style. by default dict(size=6)

legend_titlesDict[str, bool], optional

modify the each legend title. Others are the same as legend_tick_labels. by default None

legend_title_stylesDict, optional

modify the each legend title’s style. Others are the same as legend_tick_labels_styles. by default dict(size=6)

widthfloat, optional

the whole figure width, by default 8

heightfloat, optional

the whole figure height, by default 6

wspacefloat, optional

the space of whole figure at the width direction, by default 0.1. It’s the fraction of the average length of width’s axises

hspacefloat, optional

see wspace, by default 0.1

annotation_bar_widthfloat, optional

the width of Annotationbar, by default 0.03. It’s the fraction of the whole figure width

legend_bar_widthfloat, optional

the width of legend bar, by default 1.5*0.03. It’s the fraction of the whole figure width. And it’s better, set it as 1.5 * annotation_bar_width.

annotation_bar_spacefloat, optional

the space between Annotationbars, by default 0.2. It’s the fraction of the real Annotationbar width.

legend_bar_spacefloat, optional

the space between legend bars, by default 1. It’s the fraction of the real legend bar width

Figure