Circos heatmap plot for visualizing gene expressing in multiple samples.

Usage

circos_heatmap(
  data,
  low_color = "#0000ff",
  mid_color = "#ffffff",
  high_color = "#ff0000",
  gap_size = 25,
  cluster_run = TRUE,
  cluster_method = "complete",
  distance_method = "euclidean",
  dend_show = "inside",
  dend_height = 0.2,
  track_height = 0.3,
  rowname_show = "outside",
  rowname_size = 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).
low_color: Character: min value color (color name or hex value). Default: "#0000ff".
mid_color: Character: middle value color (color name or hex value). Default: "#ffffff".
high_color: Character: high value color (color name or hex value). Default: "#ff0000".
gap_size: Numeric: heatmap gap size. Default: 25, min: 0.
cluster_run: Logical: running cluster algorithm. Default: TRUE, options: TRUE, FALSE.
cluster_method: Character: cluster methods. Default: "complete", options: "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid".
distance_method: Character: distance methods. Default: "euclidean", options: "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski".
dend_show: Character: control dendgram display and position. Default: "inside", options: "none", "outside", "inside".
dend_height: Numeric: dendgram height. Default: 0.20, min: 0.00, max: 0.50.
track_height: Numeric: heatmap track height. Default: 0.30, min: 0.00, max: 0.50.
rowname_show: Character: control rownames display and position. Hind first rowname by running rownames(data). Default: "outside", options: "none", "outside", "inside".
rowname_size: Numeric: rowname font size. Default: 0.80, min: 0.10, max: 10.00.

Value

Plot: circos heatmap plot for visualizing gene expressing in multiple samples.

Author

benben-miao

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
circos_heatmap(gene_expression2[1:50,])
#> Note: 15 points are out of plotting region in sector 'group', track
#> '3'.
#> Note: 15 points are out of plotting region in sector 'group', track
#> '3'.