plot_interactions: Interaction summary plot for all cell-types and all samples...

Description Usage Arguments Value Examples

Description

Interaction summary plot for all cell-types and all samples in a dataset

Usage

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plot_interactions(x, ...)

## S4 method for signature 'ImageSet'
plot_interactions(x, label, ordering = NULL,
  normalize = TRUE, palette = NULL, celltype_order = NULL,
  xlim_fix = 13, topbar_cols = "darkgrey")

Arguments

x

IrisSpatialFeatures ImageSet object to be plotted

...

Additional arguments

label

The cell type the interaction profile should be plotted for

ordering

Ordering of the samples (default: NULL)

normalize

Normalize the interactions with a given cell-type, so they sum up to 1 (default: TRUE)

palette

Color palette for all the cell-types (default: Spectral scheme from RColorbrewer)

celltype_order

Order in which the cell-types are displayed. (default: Alphabethically)

xlim_fix

Whitespace on the right side so the legend can be displayed clearly. (default: 13)

topbar_cols

Color of the barplots that are shown on top. (default: 'darkgrey')

Value

plot of all cell-types and samples interactions

Examples

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#loading pre-read dataset
dataset <- IrisSpatialFeatures_data
dataset <- extract_interactions(dataset)
plot_interactions(dataset,'SOX10+ PDL1+',xlim_fix=3)

IrisSpatialFeatures documentation built on May 2, 2018, 2:49 a.m.