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Scatter plot showing the expression or activity of selected features on UMAP or t-SNE coordinates

feature_scatterplot.Rd

This function is used to draw a scatter plot of selected features on UMAP or t-SNE coordinates from a sparse eset object.

Usage

feature_scatterplot(
  input_eset,
  features = NULL,
  location_x = "UMAP_1",
  location_y = "UMAP_2",
  colors = NULL,
  ncol = 3,
  point.size = 0.5,
  legend.position = "right",
  legend.key_height = 3,
  legend.key_width = 1,
  fontsize.legend_title = 10,
  fontsize.legend_text = 8,
  fontsize.strip = 10,
  fontsize.axis_title = 10,
  fontsize.axis_text = 8
)

Arguments

input_eset

The expression set object that filtered, normalized and log-transformed

features

A vector of genes or drivers (row.names of the input eset) to plot

location_x

Character, name of the column of x-axis coordinates. Default: "UMAP_1".

location_y

Character, name of the column of y-axis coordinates. Default: "UMAP_2".

colors

A vector of two colors indicating the low and high values respectively. Default: c("lightgrey", "red").

ncol

Integer, number of columns when multiple plots are displayed. Default: 3.

point.size

Numeric, size of the scatter points. Default: 0.5.

legend.position

Character, position of legend: "right" (the default), "left", "top", "bottom" or "none".

legend.key_height

Numeric, height of the legend key in unit of "cm". Default: 3.

legend.key_width

Numeric, width of the legend key in unit of "cm". Default: 1.

fontsize.legend_title

Numeric, font size of the legend title. Default: 10.

fontsize.legend_text

Numeric, font size of the legend text. Default: 8.

fontsize.strip

Numeric, font size of the plot strip. Default: 10.

fontsize.axis_title

Numeric, font size of the axis label and text. Default: 10.

fontsize.axis_text

Numeric, font size of the axis label and text. Default: 8.

Value

Print a plot to screen and return a gtable containing a list of plots, can be visualized by plot(g), and saved by ggsave(file = "output.pdf", g)

Examples

data(pbmc14k_expression.eset)

## 1. scatter plots with UMAP/tSNE projections
feature_scatterplot(input_eset = pbmc14k_expression.eset,
                    features = c("CD14", "CD19", "CD8A"),
                    location_x = "UMAP_1", location_y = "UMAP_2")


## 2. change the point size and font size
feature_scatterplot(input_eset = pbmc14k_expression.eset,
                    features = c("CD14", "CD19", "CD8A"),
                    location_x = "UMAP_1", location_y = "UMAP_2",
                    point.size = 1, fontsize.strip = 12,
                    fontsize.axis_title = 10, fontsize.axis_text = 8)