plotDScoreHeatmap: Plot a heat map of the normalized drug-disease reverse...
In SubtypeDrug: Prioritization of Candidate Cancer Subtype Specific Drugs

Description Usage Arguments Details Value Author(s) Examples

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

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"
)

`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".

plotDScoreHeatmap

A heat map.

Xudong Han, Junwei Han, Chonghui Liu

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)