Heatmap cluster for visualizing clustered gene expression data.

Usage

heatmap_cluster(
  data,
  dist_method = "euclidean",
  hc_method = "average",
  k_num = 5,
  show_rownames = FALSE,
  palette = "RdBu",
  cluster_pal = "Set1",
  border_color = "#ffffff",
  angle_col = 45,
  label_size = 10,
  base_size = 12,
  line_color = "#0000cd",
  line_alpha = 0.2,
  summary_color = "#0000cd",
  summary_alpha = 0.8
)

Arguments

data: Dataframe: Shared DEGs of all paired comparisons in all samples expression dataframe of RNA-Seq. (1st-col: Genes, 2nd-col~: Samples).
dist_method: Character: distance measure method. Default: "euclidean", options: "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski".
hc_method: Character: hierarchical clustering method. Default: "average", options: "ward.D", "ward.D2", "single", "complete","average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
k_num: Numeric: the number of groups for cutting the tree. Default: 5.
show_rownames: Logical: boolean specifying if column names are be shown. Default: FALSE, options: TRUE or FALSE.
palette: Character: color palette used in heatmap. Default: "RdBu", options: 'Spectral', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn'.
cluster_pal: Character: color palette used for the cluster. Default: "Set1", options: 'Set1', 'Set2', 'Set3', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2'.
border_color: Character: cell border color (color name or hex value). Default: "#ffffff".
angle_col: Numeric: angle of the column labels. Default: 45.
label_size: Numeric: fontsize for the plot. Default: 10, min: 0.
base_size: Numeric: base font size. Default: 12, min: 0.
line_color: Character: trend lines color. Default: "#0000cd".
line_alpha: Numeric: trend lines alpha. Default: 0.20, min: 0.00, max: 1.00.
summary_color: Charater: summary line color. Default: "#0000cd".
summary_alpha: Numeric: summary line alpha. Default: 0.80, min: 0.00, max: 1.00.

Value

Plot: Heatmap cluster for visualizing clustered gene expression data.

Author

wei dong

Examples

# 1. Library TOmicsVis package
library(TOmicsVis)

# 2. Use example dataset
data(gene_expression2)
head(gene_expression2)
#>   Genes  CT_1    CT_2  CT_3 LT20_1 LT20_2 LT20_3 LT15_1 LT15_2 LT15_3 LT12_1
#> 1 ACAA2 24.50   39.83 55.38 114.11 159.32  96.88 169.56 464.84 182.66 116.08
#> 2  ACAN 14.97   18.71 10.30  71.23 142.67 213.54 253.15 320.80 104.15 174.02
#> 3  ADH1  1.54    1.56  2.04  14.95  13.60  15.87  12.80  17.74   6.06  10.97
#> 4  AHSG  0.00 1911.99  0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00
#> 5 ALDH2  2.07    2.86  2.54   0.85   0.49   0.47   0.42   0.13   0.26   0.00
#> 6 AP1S3  6.62   14.59  9.30  24.90  33.94  23.19  24.00  36.08  27.40  24.06
#>   LT12_2 LT12_3 LT12_6_1 LT12_6_2 LT12_6_3
#> 1 497.29 464.48   471.43   693.62   229.77
#> 2 305.81 469.48  1291.90   991.90   966.77
#> 3  10.71  30.95     9.84    10.91     7.28
#> 4   0.00   0.00     0.00     0.00     0.00
#> 5   0.28   0.11     0.37     0.15     0.11
#> 6  38.74  34.54    62.72    41.36    28.75

# 3. Default parameters
heatmap_cluster(gene_expression2)

#> Using Cluster, gene as id variables
#> Warning: Graphs cannot be horizontally aligned unless the axis parameter is set. Placing graphs unaligned.



# 4. Set palette = "PuOr"
heatmap_cluster(gene_expression2, palette = "PuOr")

#> Using Cluster, gene as id variables
#> Warning: Graphs cannot be horizontally aligned unless the axis parameter is set. Placing graphs unaligned.



# 5. Set line_color = "#ff0000", summary_color = "#ff0000"
heatmap_cluster(gene_expression2, line_color = "#ff0000", summary_color = "#ff0000")

#> Using Cluster, gene as id variables
#> Warning: Graphs cannot be horizontally aligned unless the axis parameter is set. Placing graphs unaligned.