Package 'CCPlotR'

Paired Arrow Plot Function

Description

This function plots interactions between a pair of cell types

Usage

cc_arrow(
  cc_df,
  cell_types = NULL,
  option = "A",
  n_top_ints = 15,
  exp_df = NULL,
  colours = setNames(paletteMartin(n = 2), cell_types),
  palette = "BuPu"
)

Arguments

cc_df	A dataframe with columns 'source', 'target', 'ligand', 'receptor' and 'score'. See toy_data for example.
cell_types	A vector of which two cell types to plot.
option	Either 'A' or 'B'. Option A will plot the top n_top_ints interactions between cell_types and their scores. Option B will plot the top n_top_ints interactions between cell_types, their scores and the expression of the ligand/receptor genes in the sender/receiver cell types.
n_top_ints	The number of top interactions to plot.
exp_df	A dataframe containing the mean expression values for each ligand/receptor in each cell type. See toy_exp for an example. Only required for option B.
colours	A named vector of colours for each cell type. Default is paletteMartin(), a colourblind-friendly palette. Only used for option A.
palette	Which colour palette to use to show the mean expression. Should be one of the RColorBrewer sequential palettes. Only used for option B.

Value

Returns a plot generated with the ggplot2 package

Examples

data(toy_data, toy_exp, package = 'CCPlotR')
cc_arrow(toy_data, cell_types = c("B", "CD8 T"), colours = c(`B` = "hotpink", `CD8 T` = "orange"))
cc_arrow(toy_data,
    cell_types = c("NK", "CD8 T"), option = "B", exp_df = toy_exp,
    n_top_ints = 10, palette = "OrRd"
)

---

Circos Plot Function

Description

This function creates a circos plot

Usage

cc_circos(
  cc_df,
  option = "A",
  n_top_ints = 15,
  exp_df = NULL,
  cell_cols = NULL,
  palette = "BuPu",
  cex = 1,
  show_legend = TRUE,
  scale = FALSE,
  ...
)

Arguments

cc_df	A dataframe with columns 'source', 'target', 'ligand', 'receptor' and 'score'. See toy_data for example.
option	Either 'A' , 'B' or 'C'. Option A will plot the number of interactions between pairs of cell types, option B will plot the top n_top_ints interactions and their scores. Option C will plot the top n_top_ints interactions, their scores and the mean expression of the ligands/receptors in the sending/receiver cell types.
n_top_ints	The number of top interactions to plot. Only required for options B and C.
exp_df	A dataframe containing the mean expression values for each ligand/receptor in each cell type. See toy_exp for an example. Only required for option C.
cell_cols	A named vector of colours for each cell type. Default uses paletteMartin(), a colourblind-friendly palette.
palette	Which colour palette to use to show the mean expression. Should be one of the RColorBrewer sequential palettes.
cex	Determines text size
show_legend	TRUE or FALSE - whether to add legend or not. Only required for options B and C.
scale	TRUE or FALSE - whether to scale each sector to same width. Only required for options B and C.
...	Additional parameters passed to chordDiagram function.

Value

Returns a chord diagram generated by the circlize R package

Examples

data(toy_data, toy_exp, package = 'CCPlotR')
cc_circos(toy_data)
cc_circos(toy_data, option = "B", n_top_ints = 10, cex = 0.5)
cc_circos(toy_data,
    option = "C", n_top_ints = 15, exp_df = toy_exp,
    cell_cols = c(`B` = "hotpink", `NK` = "orange", `CD8 T` = "cornflowerblue"),
    palette = "PuRd", cex = 0.5
)

---

Dotplot Function

Description

This function plots a dotplot

Usage

cc_dotplot(cc_df, option = "A", n_top_ints = 30)

Arguments

cc_df	A dataframe with columns 'source', 'target', 'ligand', 'receptor' and 'score'. See toy_data for example.
option	Either 'A', 'B', 'CellPhoneDB' or 'Liana'. Option A will plot the number of interactions between pairs of cell types, option B will plot the top n_top_ints interactions and their scores. The 'CellPhoneDB' and 'Liana' options will generate a dotplot in the style of these popular tools.
n_top_ints	The number of top interactions to plot. Only required for option B.

Value

Returns a plot generated with the ggplot2 package

Examples

data(toy_data, package = 'CCPlotR')
cc_dotplot(toy_data)
cc_dotplot(toy_data, option = "B", n_top_ints = 10)
cc_dotplot(toy_data, option = "Liana", n_top_ints = 15)

---

Heatmap Function

Description

This plots a heatmap

Usage

cc_heatmap(cc_df, option = "A", n_top_ints = 30)

Arguments

cc_df	A dataframe with columns 'source', 'target', 'ligand', 'receptor' and 'score'. See toy_data for example.
option	Either 'A', 'B', 'CellPhoneDB' or 'Liana'. Option A will plot the number of interactions between pairs of cell types, option B will plot the top n_top_ints interactions and their scores. The 'CellPhoneDB' and 'Liana' options will generate a heatmap in the style of these popular tools.
n_top_ints	The number of top interactions to plot. Only required for option B.

Value

Returns a plot generated with the ggplot2 package

Examples

data(toy_data, package = 'CCPlotR')
cc_heatmap(toy_data)
cc_heatmap(toy_data, option = "B", n_top_ints = 10)
cc_heatmap(toy_data, option = "CellPhoneDB")

---

Network Plot Function

Description

This function plots a network of representing the number of interactions between cell types

Usage

cc_network(
  cc_df,
  colours = paletteMartin(),
  option = "A",
  n_top_ints = 20,
  node_size = 2.75,
  label_size = 4,
  layout = "kk"
)

Arguments

cc_df	A dataframe with columns 'source', 'target', 'ligand', 'receptor' and 'score'. See toy_data for example.
colours	A vector of colours for each cell type. Default is paletteMartin(), a colourblind-friendly palette.
option	Either 'A' or 'B'. Option A will plot the number of interactions between pairs of cell types, option B will plot the top n_top_ints interactions and their scores.
n_top_ints	The number of top interactions to plot. Only required for option B.
node_size	Point size for nodes in option B.
label_size	Size for labels in option B.
layout	Algorithm for determining layout in option B. One of 'dh', 'drl', 'fr', 'gem', 'graphopt', 'kk', 'lgl', 'mds', 'nicely'. See iGraph layouts for more details.

Value

Returns a plot generated with the ggplot2 package

Examples

data(toy_data, package = 'CCPlotR')
cc_network(toy_data)
cc_network(toy_data, colours = c("orange", "cornflowerblue", "hotpink"), option = "B")

---

Sigmoid Plot Function

Description

This function plots interactions using the geom_sigmoid function from the ggbump R package

Usage

cc_sigmoid(cc_df, n_top_ints = 20, colours = paletteMartin())

Arguments

cc_df	A dataframe with columns 'source', 'target', 'ligand', 'receptor' and 'score'. See toy_data for example.
n_top_ints	The number of top interactions to plot.
colours	A named vector of colours for each cell type. Default is paletteMartin(), a colourblind-friendly palette.

Value

Returns a plot generated with the ggplot2 package

Examples

data(toy_data, package = 'CCPlotR')
cc_sigmoid(toy_data)
cc_sigmoid(toy_data, colours = c(
    `B` = "hotpink", `CD8 T` = "orange",
    `NK` = "cornflowerblue"
), n_top_ints = 25)

---

geom_sigmoid This function is copied from the ggbump package

Description

Creates a ggplot that makes a smooth rank over time. To change the smooth argument you need to put it outside of the aes of the geom. Uses the x, xend, y and yend aestethics. Make sure each sigmoid curve is its own group.

Usage

geom_sigmoid(
  mapping = NULL,
  data = NULL,
  geom = "line",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  smooth = 8,
  direction = "x",
  inherit.aes = TRUE,
  ...
)

Arguments

mapping	provide you own mapping. both x, xend, y and yend need to be numeric.
data	provide you own data
geom	xhange geom
position	change position
na.rm	remove missing values
show.legend	show legend in plot
smooth	how much smooth should the curve have? More means steeper curve.
direction	the character x or y depending of smoothing direction
inherit.aes	should the geom inherits aestethics
...	other arguments to be passed to the geom

Value

ggplot layer

Examples

library(ggplot2)
df <- data.frame(x = 1:6,
       y = 5:10,
       xend = 7,
       yend = -3:2)

ggplot(df, aes(x = x, xend = xend, y = y, yend = yend, color = factor(x))) +
  geom_sigmoid()

---

Discrete palette generator

Description

Generate a palette of up to 15 colours. The colours are from the paletteMartin palette in the colorBlindess R package.

Usage

paletteMartin(n = 15)

Arguments

n	Number of colours to return. Max = 15.

Value

Returns a vector of colours of length n.

Examples

scales::show_col(paletteMartin(n = 9))

---

This function is copied from the ggbump package

Description

This function is copied from the ggbump package

---

Toy data for CCPlotR

Description

A toy dataset of ligand-receptor interactions to demonstrate cell-cell interaction plots.

Usage

toy_data

Format

An object of class tbl_df (inherits from tbl, data.frame) with 735 rows and 5 columns.

Value

toy_data

A data frame with 735 rows and 5 columns:

source

Cell type expressing the ligand

target

Cell type expressing the receptor

ligand

Ligand

receptor

Receptor

score

A score for each interaction e.g. -log10(aggregate_rank) returned by Liana

Source

This is a modified version of the toy dataset that comes with the Liana R package.

---

Toy expression data for CCPlotR

Description

A dataframe showing the mean expression values for each ligand and receptor in each cell type.

Usage

toy_exp

Format

An object of class grouped_df (inherits from tbl_df, tbl, data.frame) with 477 rows and 3 columns.

Value

toy_exp

A data frame with 477 rows and 3 columns:

cell_type

Cell type

gene

Ligand/receptor gene

mean_exp

Mean (normalised) expression of lignad/receptor gene in cell type

---