Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.

Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.

Usage

gene_cluster_trend(
  data,
  thres = 0.25,
  min_std = 0.2,
  palette = "PiYG",
  cluster_num = 4
)

Arguments

data

Dataframe: Shared DEGs of all paired comparisons in all groups expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~n-1-col: Groups, n-col: Pathways).

thres

Number: set the threshold for excluding genes. Default: 0.25.

min_std

Number: set the threshold for minimum standard deviation. Default: 0.2.

palette

Character: set the color palette to be used for plotting. Default: "PiYG", options: 'Spectral', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'.

cluster_num

Number: set the number of clusters. Default: 4.

Value

Plot: Gene cluster trend plot for visualizing gene expression trend profile in multiple samples.

Author

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset gene_cluster_data
data(gene_expression3)
head(gene_expression3)
#>   Genes         CT        LT20     LT15      LT12      LT12_6
#> 1 ACAA2  39.903333 123.4366667 272.3533 359.28333  464.940000
#> 2  ACAN  14.660000 142.4800000 226.0333 316.43667 1083.523333
#> 3  ADH1   1.713333  14.8066667  12.2000  17.54333    9.343333
#> 4  AHSG 637.330000   0.0000000   0.0000   0.00000    0.000000
#> 5 ALDH2   2.490000   0.6033333   0.2700   0.13000    0.210000
#> 6 AP1S3  10.170000  27.3433333  29.1600  32.44667   44.276667
#>                 Pathways
#> 1 PPAR signaling pathway
#> 2 PPAR signaling pathway
#> 3 PPAR signaling pathway
#> 4 PPAR signaling pathway
#> 5 PPAR signaling pathway
#> 6 PPAR signaling pathway

# 3. Default parameters
gene_cluster_trend(gene_expression3[,-7])
#> 0 genes excluded.
#> 0 genes excluded.

#> NULL

# 4. Set palette = "RdBu"
gene_cluster_trend(gene_expression3[,-7], palette = "RdBu")
#> 0 genes excluded.
#> 0 genes excluded.

#> NULL

# 5. Set cluster_num = 6
gene_cluster_trend(gene_expression3[,-7], cluster_num = 6, palette = "Spectral")
#> 0 genes excluded.
#> 0 genes excluded.

#> NULL