umap_plot {TOmicsVis}

UMAP plot for analyzing and visualizing UMAP algorithm.

Description

UMAP plot for analyzing and visualizing UMAP algorithm.

Usage

umap_plot(
  sample_gene,
  group_sample,
  seed = 1,
  multi_shape = TRUE,
  point_size = 5,
  point_alpha = 1,
  text_size = 5,
  text_alpha = 0.8,
  fill_alpha = 0,
  border_alpha = 0,
  sci_fill_color = "Sci_AAAS",
  legend_pos = "right",
  legend_dir = "vertical",
  ggTheme = "theme_light"
)

Arguments

sample_gene

Dataframe: gene expression dataframe (1st-col: Transcripts or Genes, 2nd-col~: Samples).

group_sample

Dataframe: Samples and groups for gene expression (1st-col: Samples, 2nd-col: Groups).

seed

Numeric: set seed for robust result. Default: 1.

multi_shape

Logical: groups as shapes. Default: FALSE, options: TRUE, FALSE.

point_size

Numeric: point size. Default: 5, min: 0, max: null.

point_alpha

Numeric: point color alpha. Default: 0.80, min: 0.00, max: 1.00.

text_size

Numeric: text size. Default: 5, min: 0 (hind), max: null.

text_alpha

Numeric: text alpha. Default: 0.80, min: 0.00, max: 1.00.

fill_alpha

Numeric: ellipse alpha. Default: 0.30, min: 0.00, max: 1.00.

border_alpha

Numeric: ellipse border color alpha. Default: 0.10, min: 0.00, max: 1.00.

sci_fill_color

Character: ggsci color pallet. Default: "Sci_AAAS", options: "Sci_AAAS", "Sci_NPG", "Sci_Simpsons", "Sci_JAMA", "Sci_GSEA", "Sci_Lancet", "Sci_Futurama", "Sci_JCO", "Sci_NEJM", "Sci_IGV", "Sci_UCSC", "Sci_D3", "Sci_Material".

legend_pos

Character: legend position. Default: "right", options: "none", "left", "right", "bottom", "top".

legend_dir

Character: legend direction. Default: "vertical", options: "horizontal", "vertical".

ggTheme

Character: ggplot2 themes. Default: "theme_light", options: "theme_default", "theme_bw", "theme_gray", "theme_light", "theme_linedraw", "theme_dark", "theme_minimal", "theme_classic", "theme_void"

Value

Plot: UMAP plot for analyzing and visualizing UMAP algorithm.

Author(s)

benben-miao

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_expression)
head(gene_expression)

data(samples_groups)
head(samples_groups)

# 3. Default parameters
umap_plot(gene_expression, samples_groups)

# 4. Set sci_fill_color = "Sci_Simpsons", seed = 6
umap_plot(gene_expression, samples_groups, sci_fill_color = "Sci_Simpsons", seed = 6)

# 5. Set fill_alpha = 0.10
umap_plot(gene_expression, samples_groups, fill_alpha = 0.10)