scimap.pl.spatial_interaction
Function Call
scimap.pl.spatial_distance
(
adata,
spatial_distance='spatial_distance',
phenotype='phenotype', imageid='imageid', log=False,
method='heatmap', heatmap_summarize=True,
heatmap_na_color='grey',heatmap_cmap='vlag_r',
heatmap_row_cluster=False, heatmap_col_cluster=False,
heatmap_standard_scale=0, distance_from=None,
distance_to=None, x_axis = None, y_axis = None,
facet_by = None, plot_type = None,
kwargs **)
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')