plot2D: Visualization of 2D data of FSPY

Description Usage Arguments Value Examples

View source: R/plot2D.R

Description

Visualization of 2D data of FSPY

Usage

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plot2D(
  object,
  item.use = c("PC_1", "PC_2"),
  color.by = "stage",
  order.by = NULL,
  size = 1,
  alpha = 1,
  category = "categorical",
  show.cluser.id = FALSE,
  show.cluser.id.size = 4,
  main = "2D plot of FSPY",
  plot.theme = theme_bw()
)

Arguments

object

An FSPY object

item.use

character. Items use to 2D plot, axes x and y must be numeric.

color.by

character. Dot or mesh color by which character. It can be one of the column of plot.meta, or it can be just "density" (the default value).

order.by

vector. Order of color theme.

size

numeric. Size of the dot

alpha

numberic. Transparency (0-1) of the dot, default is 1.

category

character. numeric or categorical

show.cluser.id

logical. Whether to show cluster id in the plot.

show.cluser.id.size

numeric. Size of the cluster id.

main

character. Title of the plot.

plot.theme

themes from ggplot2

Value

ggplot2 figure

Examples

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if (FALSE) {

# Default plot
plot2D(fspy)

# PCA plot
plot2D(fspy, item.use = c("PC_1", "PC_2"))
plot2D(fspy, item.use = c("PC_1", "PC_2"), color.by = "cluster.id")
plot2D(fspy, item.use = c("PC_1", "PC_2"), color.by = "stage")
plot2D(fspy, item.use = c("PC_2", "PC_3"), color.by = "stage") +
  scale_color_manual(values = c("#00599F","#009900","#FF9933",
                                "#FF99FF","#7A06A0","#FF3222"))
plot2D(fspy, item.use = c("PC_2", "PC_3"), color.by = "CD43",
       category = "numeric")
plot2D(fspy, item.use = c("PC_2", "PC_3"), color.by = "CD43",
       category = "numeric") +
       scale_colour_gradientn(colors = c("blue","white","red"))

# tSNE plot
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"))
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"), color.by = "stage")
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"), color.by = "cluster.id",
       alpha = 0.5, main = "tSNE Plot")
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"), color.by = "cluster.id",
       alpha = 1, main = "tSNE Plot", show.cluser.id = T)
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"), color.by = "CD43",
       category = "numeric", size = 3) +
       scale_colour_gradientn(colors = c("blue","white","red"))
plot2D(fspy, item.use = c("tSNE_1", "tSNE_2"), color.by = "stage") +
  scale_color_manual(values = c("#00599F","#009900","#FF9933",
                                "#FF99FF","#7A06A0","#FF3222"))

# Diffusion Map plot
plot2D(fspy, item.use = c("DC_1", "DC_2"))
plot2D(fspy, item.use = c("DC_1", "DC_2"), color.by = "stage")
plot2D(fspy, item.use = c("DC_2", "DC_3"), color.by = "cluster.id",
       alpha = 0.5, main = "Diffusion Map Plot")
plot2D(fspy, item.use = c("DC_2", "DC_3"), color.by = "cluster.id",
       alpha = 1, main = "Diffusion Map Plot", show.cluser.id = T)
plot2D(fspy, item.use = c("DC_1", "DC_2"), color.by = "CD43",
       category = "numeric", size = 3) +
       scale_colour_gradientn(colors = c("blue","white","red"))

# UMAP plot
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"))
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"), color.by = "stage")
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"), color.by = "cluster.id",
       alpha = 0.5, main = "UMAP Plot")
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"), color.by = "cluster.id",
       alpha = 1, main = "UMAP Plot", show.cluser.id = T)
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"), color.by = "CD43",
       category = "numeric", size = 3) +
       scale_colour_gradientn(colors = c("blue","white","red"))
plot2D(fspy, item.use = c("UMAP_1", "UMAP_2"), color.by = "stage") +
  scale_color_manual(values = c("#00599F","#009900","#FF9933",
                                "#FF99FF","#7A06A0","#FF3222"))

# Marker Plot
plot2D(fspy, item.use = c("CD43", "CD90"), color.by = "cluster.id")
plot2D(fspy, item.use = c("CD34", "CD90"), color.by = "CD43",
       category = "numeric", size = 3) +
       scale_colour_gradientn(colors = c("blue","white","red"))

# Pseudotime
plot2D(fspy, item.use = c("pseudotime", "CD43"), color.by = "stage")

}

flowSpy documentation built on Nov. 8, 2020, 6:53 p.m.