plotDScoreHeatmap {SubtypeDrug}

Plot a heat map of the normalized drug-disease reverse association scores for cancer samples

Description

According to the parameter setting, the function 'plotDScoreHeatmap()' displays the heat map of the normalized drug-disease reverse association score for the significant drugs.

Usage

plotDScoreHeatmap(
  data,
  subtype.label = "all",
  SDS = "all",
  E_Pvalue.th = 1,
  E_FDR.th = 0.05,
  S_Pvalue.th = 1,
  S_FDR.th = 0.001,
  show.rownames = TRUE,
  show.colnames = FALSE,
  color = colorRampPalette(c("#0A8D0A", "#F8F0EB", "red"))(190),
  subtype_colors = NA,
  drug_colors = NA,
  border_color = "grey60",
  cellwidth = NA,
  cellheight = NA,
  fontsize = 10,
  fontsize.row = 10,
  fontsize.col = 10,
  scale = "row"
)

Arguments

data

A list of result data generated by function 'PrioSubtypeDrug()'.

subtype.label

Character string indicates which sample of the cancer subtype was used to plot the heat map. If subtype.label = "all" (default), all cancer samples will be shown in the heat map.

SDS

A string indicates that the range of SDS is used for the heat map. if SDS="all" (default), the SDS will not be filtered. SDS="negative", only drugs with SDS<0 are used. SDS="positive", only drugs with SDS>0 are used.

E_Pvalue.th

A numeric.A threshold is used to filter the drug effected P value (default: 1).

E_FDR.th

A numeric.A threshold is used to filter the drug effected FDR (default: 0.05).

S_Pvalue.th

A numeric.A threshold is used to filter the Subtype specific P value (default: 1).

S_FDR.th

A numeric.A threshold is used to filter the Subtype specific P value (default: 0.001).

show.rownames

Boolean specifying if row names are be shown (default: TRUE).

show.colnames

Boolean specifying if column names are be shown (default: FALSE).

color

Vector of colors used in heatmap.

subtype_colors

Vector of colors is used to annotate the sample subtype. Its length should correspond to the number of sample subtypes.

drug_colors

Vector of colors is used to label subtype-specific drugs.

border_color

Color of cell borders on heatmap, use NA if no border should be drawn.

cellwidth

Individual cell width in points. If left as NA, then the values depend on the size of plotting window.

cellheight

Individual cell height in points. If left as NA, then the values depend on the size of plotting window.

fontsize

Base fontsize for the plot (default: 10).

fontsize.row

Fontsize for rownames (default: 10).

fontsize.col

Fontsize for colnames (default: 10).

scale

Character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. Corresponding values are "row" (default), "column" and "none".

Details

plotDScoreHeatmap

Value

A heat map.

Author(s)

Xudong Han, Junwei Han, Chonghui Liu

Examples

require(pheatmap)
## Get the result data of PrioSubtypeDrug().
## The data is based on the simulated breast cancer subtype data.
Subtype_drugs<-get("Subtype_drugs")
## Heat map of all subtype-specific drugs.
#plotDScoreHeatmap(data=Subtype_drugs,E_Pvalue.th=0.05,
#                           S_Pvalue.th=0.05)
## Plot only Basal subtype-specific drugs.
plotDScoreHeatmap(Subtype_drugs,subtype.label="Basal",SDS="all",E_Pvalue.th=0.05,
                  E_FDR.t=1,S_Pvalue.th=0.05,S_FDR.th=1)