plotDSpwHeatmap: Plot heat map of the drug regulated subpathway activity score

In SubtypeDrug: Prioritization of Candidate Cancer Subtype Specific Drugs

Description

The 'plotDSpwHeatmap()' function plots a heat map of the subpathways that are regulated by specified drug and have differential expression between specified cancer subtype and normal.

Usage

plotDSpwHeatmap(
  data,
  drug.label = "",
  subtype.label = "",
  show.rownames = TRUE,
  show.colnames = TRUE,
  color = NA,
  phen_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()'.
drug.label	A character string of drug labels to determine which drug to use for visualization.
subtype.label	Character string indicates which sample of the cancer subtype was used to plot the heat map.
show.rownames	Boolean specifying if row names are be shown.
show.colnames	Boolean specifying if column names are be shown.
color	Vector of colors used in heatmap.
phen_colors	Vector of colors is used to annotate the sample subtype and control sample.It should be assigned two colors.
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", "column" and "none".

Details

plotDSpwHeatmap

Based on the input cancer subtype, the program draws a heat map of the drug regulated subpathway activity score. If the cancer subtype of input has sutype-specific drug score (SDS)<0, we can observe the drug upregulatory subpathway is lowly expressed in the cancer subtype samples and high in the normal samples; the drug downregulatory subpathway is highly expressed in the cancer subtype samples and low in the normal samples. This indicates that after the drug action, these subpathways activity is converted from the level of the cancer subtype into the level of normal. If the cancer subtype of input has sutype-specific drug score (SDS)>0, it is indicated that the drug action may promote the subpathway expression status of the cancer subtype.

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")
plotDSpwHeatmap(data=Subtype_drugs,drug.label="pirenperone(1.02e-05M)",subtype.label="Basal")
##Visualize the results of only two types of samples.
Disease_drugs<-get("Disease_drugs")
plotDSpwHeatmap(data=Disease_drugs,drug.label="W-13(1e-05M)",subtype.label="Cancer")

SubtypeDrug documentation built on May 17, 2021, 9:09 a.m.