tsne_analysis {TOmicsVis}

TSNE analysis for analyzing and visualizing TSNE algorithm.

Description

TSNE analysis for analyzing and visualizing TSNE algorithm.

Usage

tsne_analysis(sample_gene, group_sample, seed = 1, tsne_dims = 2)

Arguments

sample_gene

Dataframe: All genes in all samples expression dataframe of RNA-Seq (1st-col: 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.

tsne_dims

Numeric: TSNE dimensionality number. Default: 2.

Value

Table: TSNE analysis for analyzing and visualizing TSNE 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
res <- tsne_analysis(gene_expression, samples_groups)
head(res)

# 4. Set tsne_dims = 3
res <- tsne_analysis(gene_expression, samples_groups, tsne_dims = 3)
head(res)