scimap.pl.spatial_interaction

Short description

The spatial_distance plotting function allows users to generate a heatmap to visualize spatial interaction output from sm.tl.spatial_interaction. The intensity represents number of interactions (scaled) and blank regions represent non-significant results.

Parameters

adata : AnnData object

spatial_distance: string (The default is 'spatial_distance')
In order to locate the spatial_distance data within the AnnData object please provide the output label/columnname of sm.tl.spatial_distance function.

phenotype : string, required (The default is 'phenotype')
Column name of the column containing the phenotype information. It could also be any categorical assignment given to single cells.

imageid : string, optional (The default is 'imageid')
Column name of the column containing the image id.

log : bool, optional (The default is False)
Convert distance to log scale.

method : string, optional (The default is 'heatmap')
Three options are available.
1) heatmap - generates a heatmap of average shortest distance between all phenotypes.
2) numeric - can be used to generate boxplot, violin plot etc between a given set of phenotypes.
3) distribution - can be used to generate distribution plots between a given set of phenotypes.

heatmap_summarize : bool, optional (The default is True)
In the event multiple images are present in the dataset, True allows to calculate the average across all the images.

heatmap_na_color : string, optional (The default is 'grey')
Color for NA values within the heatmap.

heatmap_row_cluster : bool, optional (The default is False)
Cluster Rows.

heatmap_col_cluster : bool, optional (The default is False)
Cluster Columns.

heatmap_cmap : string, optional (The default is 'vlag')
Color map to use for continous variables. Can be a name or a Colormap instance (e.g. 'magma', 'viridis').

heatmap_standard_scale : int, optional (The default is 0)
Either 0 (rows) or 1 (columns). Whether or not to standardize that dimension, meaning for each row or column, subtract the minimum and divide each by its maximum. The default is 0.

distance_from : string, optional (The default is None)
In the event of using method = 'numeric' or 'distribution', this argument is required.
Pass a phenotype of interest. If distance_from is provided and distance_to is not provided, the function will plot the average distance from the phenotype of interest to all phenotypes present within the dataset.

distance_to : string, optional (The default is None)
In the event of using method = 'numeric' or 'distribution', this argument is required.
Pass a phenotype of interest. The function will plot the average shortest between two phenotypes of interest (distance_from and distance_to).

x_axis : string, optional (The default is distance)
In the event of using method = 'numeric' or 'distribution', this argument is required. This determines the elements present in the x-axis of the resultant plot.
Allowed arguments are: 'group', 'distance', 'imageid'.

y_axis : string, optional (The default is group)
In the event of using method = 'numeric' or 'distribution', this argument is required. This determines the elements present in the y-axis of the numeric plot and if the user uses the distribution plot this argument is used to overlaying multiple categories within the same distribution plot.
Allowed arguments are: 'group', 'distance', 'imageid'.

facet_by : string, optional (The default is None)
In the event of using method = 'numeric' or 'distribution', this argument can be used to generate sub-plots. Allowed arguments are: 'group', 'imageid'.

plot_type : string, optional (The default is None)
In the event of using method = 'numeric' or 'distribution', this argument is required.
- For numeric plot, the following options are available: “strip”, “swarm”, “box”, “violin”, “boxen”, “point”, “bar”, or “count”.
- For distribution plot, the following options are available: “hist”, “kde”, “ecdf”.
1) The default for numeric plot is 'boxen'.
2) The default for distribution plot is 'kde`.

**kwargs: key:value pairs.
Are passed to sns.clustermap. Pass other parameters that works with sns.clustermap, sns.catplot or sns.displot e.g. linecolor='black'

Returns

Heatmap or Numeric Plot or Distribution Plot.

Example

# summary heatmap
sm.pl.spatial_distance (adata)

# Heatmap without summarizing the individual images
sm.pl.spatial_distance (adata, heatmap_summarize=False, imageid='ImageId')

# Numeric plot of shortest distance of phenotypes from tumor cells
sm.pl.spatial_distance (adata, method='numeric',distance_from='Tumor CD30+',imageid='ImageId')

# Distribution plot of shortest distance of phenotypes from tumor cells
sm.pl.spatial_distance (adata, method='distribution',distance_from='Tumor CD30+',imageid='ImageId', x_axis="distance", y_axis="imageid", plot_type="kde")

# Numeric plot of shortest distance of phenotypes from tumor cells to M2 Macrophages
sm.pl.spatial_distance (adata, method='numeric',distance_from='Tumor CD30+',distance_to = 'M2 Macrophages', imageid='ImageId')

# Distribution plot of shortest distance of phenotypes from tumor cells to M2 Macrophages
sm.pl.spatial_distance (adata, method='distribution',distance_from='Tumor CD30+',distance_to = 'M2 Macrophages',imageid='ImageId')