heatmap.ggplot2 — heatmap.ggplot2 • BS831

heatmap.ggplot2 is the main function to draw and/or save the heatmap from an expression set object

heatmap.ggplot2(
  eSet,
  brewer.pal.name = "RdBu",
  brewer.pal.rev = TRUE,
  brewer.numColors = 11,
  col.legend.brewer = "",
  row.legend.brewer = "",
  col.clust = TRUE,
  row.clust = TRUE,
  col.clust.hc = NA,
  row.clust.hc = NA,
  col.lab = "",
  row.lab = "",
  heatmap.y.text = FALSE,
  heatmap.x.text = FALSE,
  heatmap.y.text.size = 7,
  heatmap.x.text.size = 6,
  heatmap.colorlegend.name = "val",
  title.text = "",
  col.legend.name = "",
  row.legend.name = "",
  legend.lab.max.char = 15,
  row.scaling = "none",
  z.norm = FALSE,
  cuttree.col = 0,
  cuttree.row = 0,
  verbose = FALSE,
  grid.heights = NA,
  grid.widths = NA,
  show = FALSE
)

Arguments

eSet	expression set object to plot
brewer.pal.name	name of colorbrewer, see options at RColorBrewer::display.brewer.all()
brewer.pal.rev	reverse colorbrewer (TRUE or FALSE)
brewer.numColors	number of colors for heatmap palette default 11
col.legend.brewer	string vector of hexdecimal values for column labels, see example p3 and p4 for how to determine annotation labels and assigning colors
row.legend.brewer	string vector of hexdecimal values for row labels
col.clust	perform column-wise hierarchical clustering (TRUE or FALSE)
row.clust	perform row-wise hierarchical clustering (TRUE or FALSE)
col.clust.hc	hc object to be passed to as.dendrogram, available when col.clust = TRUE, default NA: hc.col = hcopt(stats::dist(t(x)), method="ward.D")
row.clust.hc	hc object to be passed to as.dendrogram, available when row.clust = TRUE, default NA: hc.row = hcopt(stats::as.dist(1-cor(t(x))),method="ward.D")
col.lab	column labels to include: subset of pData colnames character vector
row.lab	row labels to include: subset of fData colnames character vector
heatmap.y.text	include y axis labels for heatmap, uses rownames(eSet) (TRUE or FALSE)
heatmap.x.text	include x axis labels for heatmap, uses colnames(eSet)) (TRUE or FALSE)
heatmap.y.text.size	text size for y axis labels
heatmap.x.text.size	text size for x axis labels
heatmap.colorlegend.name	name for heatmap color legend
title.text	main title for the plot
col.legend.name	character vector for subset of col.lab to include in color legend
row.legend.name	character vector for subset of row.lab to include in color legend
legend.lab.max.char	number of characters limit for legend labels, default = 15
row.scaling	how should rows be scaled ("none", "quantile", "z-score.all", or "z-score.capped")
z.norm	heatmap colors reflect z-scores rather than original values, can be TRUE if row.scaling is "none"
cuttree.col	number of clusters for columns, default 0: do not show cluster assignment
cuttree.row	number of clusters for rows, default 0: do not show cluster assignment
verbose	return additional clustred annotation information as well as heatmap
grid.heights	numeric vector of length 7 representing heights of subpanels, leave NA for default
grid.widths	numeric vector of length 4 represeting weights of subpanels, leave NA for default
show	prints the heatmap within execution of the function (TRUE or FALSE)

Examples


#Use example data #1, for data set information: ?eSet1
data(eSet.brca.100)
#> Warning: data set ‘eSet.brca.100’ not found
eSet1<-eSet.brca.100
#> Error in eval(expr, envir, enclos): object 'eSet.brca.100' not found
eSet1<-eSet1[1:10,1:25]
#> Error in eval(expr, envir, enclos): object 'eSet1' not found

p1<-heatmap.ggplot2(eSet=eSet1, col.clust = TRUE, row.clust = TRUE, 
col.clust.hc = NA, row.clust.hc = NA,
col.lab = c("HER2_status", "ER_status", "PR_status", "TN_status"), row.lab = "", 
heatmap.y.text = TRUE, heatmap.x.text = TRUE,
heatmap.colorlegend.name = "RNASeq_expression",
title.text = "TCGA BRCA log2 RNA-seq expression, z-score row normalized",
col.legend.name = c("HER2_status", "ER_status", "PR_status", "TN_status"), 
row.legend.name = "", 
row.scaling = "z-score.capped", 
z.norm = FALSE, 
cuttree.col = 4, cuttree.row = 3,
verbose = FALSE, show = FALSE)
#> Warning: `axis.ticks.margin` is deprecated. Please set `margin` property of `axis.text` instead
#> Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
#> Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'eSet1' not found
grid.arrange(p1)
#> Error in grid.arrange(p1): could not find function "grid.arrange"


x<-exprs(eSet1)
#> Error in exprs(eSet1): could not find function "exprs"
hc.row<-hcopt(stats::as.dist(1-cor(t(x))),method="ward.D")
#> Error in t(x): object 'x' not found
hc.col <- hcopt(stats::dist(t(x), method = "euclidean"), method="ward.D") 
#> Error in t(x): object 'x' not found

#Adding custom hclust object in col.clust.hc and row.clust.hc
p2 <- heatmap.ggplot2(eSet=eSet1, col.clust = TRUE, row.clust = TRUE, 
col.clust.hc = hc.col, row.clust.hc = hc.row,
col.lab = c("HER2_status", "ER_status", "PR_status", "TN_status"), row.lab = "", 
heatmap.y.text = TRUE, heatmap.x.text = TRUE,
heatmap.colorlegend.name = "RNASeq_expression",
title.text = "TCGA BRCA log2 RNA-seq expression, z-score row normalized",
col.legend.name = c("HER2_status", "ER_status", "PR_status", "TN_status"), 
row.legend.name = "", 
row.scaling = "z-score.capped", 
z.norm = FALSE, 
cuttree.col = 4, cuttree.row = 3,
verbose = FALSE, show = FALSE)
#> Warning: `axis.ticks.margin` is deprecated. Please set `margin` property of `axis.text` instead
#> Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
#> Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'eSet1' not found
grid.newpage()
#> Error in grid.newpage(): could not find function "grid.newpage"
grid.arrange(p2)
#> Error in grid.arrange(p2): could not find function "grid.arrange"


#Saving plot in verbose format
p3 <- heatmap.ggplot2(eSet=eSet1, col.clust = TRUE, row.clust = TRUE, 
col.clust.hc = hc.col, row.clust.hc = hc.row,
col.lab = c("HER2_status", "ER_status", "PR_status", "TN_status"), row.lab = "", 
heatmap.y.text = TRUE, heatmap.x.text = TRUE,
heatmap.colorlegend.name = "RNASeq_expression",
title.text = "TCGA BRCA log2 RNA-seq expression, z-score row normalized",
col.legend.name = c("HER2_status", "ER_status", "PR_status", "TN_status"), 
row.legend.name = "", 
row.scaling = "z-score.capped", 
z.norm = FALSE, 
cuttree.col = 4, cuttree.row = 3,
verbose = TRUE, show = FALSE)
#> Warning: `axis.ticks.margin` is deprecated. Please set `margin` property of `axis.text` instead
#> Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
#> Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'eSet1' not found
grid.newpage()
#> Error in grid.newpage(): could not find function "grid.newpage"
grid.arrange(p3$heatmap)
#> Error in grid.arrange(p3$heatmap): could not find function "grid.arrange"


#Adding custom colors to column and row annotation labels
print(p3$meta.c$id)
#> Error in print(p3$meta.c$id): object 'p3' not found
meta.c.color.string<-c("yellow", "khaki3", "gold", "chocolate", "darkred", "cyan")
meta.c.color<-as.character(sapply(meta.c.color.string, to.hex))
names(meta.c.color)<-c("Negative", "Positive", "1", "2", "3", "4")
print(p3$meta.r$id)
#> Error in print(p3$meta.r$id): object 'p3' not found
meta.r.color.string<-c("pink", "azure", "green")
meta.r.color<-as.character(sapply(meta.r.color.string, to.hex))
names(meta.r.color)<-c("1", "2", "3")

p4<-heatmap.ggplot2(eSet=eSet1, 
col.legend.brewer = meta.c.color,
row.legend.brewer = meta.r.color,
col.clust = TRUE, row.clust = TRUE, 
col.clust.hc = hc.col, row.clust.hc = hc.row,
col.lab = c("HER2_status", "ER_status", "PR_status", "TN_status"), row.lab = "cluster.row", 
heatmap.y.text = TRUE, heatmap.x.text = TRUE,
heatmap.colorlegend.name = "RNASeq_expression",
title.text = "TCGA BRCA log2 RNA-seq expression, z-score row normalized",
col.legend.name = c("HER2_status", "ER_status", "PR_status", "TN_status", "cluster.col"), 
row.legend.name = "cluster.row", 
row.scaling = "z-score.capped", 
z.norm = FALSE, 
cuttree.col = 4, cuttree.row = 3,
verbose = FALSE, show = FALSE)
#> Warning: `axis.ticks.margin` is deprecated. Please set `margin` property of `axis.text` instead
#> Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
#> Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'exprs': object 'eSet1' not found
grid.newpage()
#> Error in grid.newpage(): could not find function "grid.newpage"
grid.arrange(p4)
#> Error in grid.arrange(p4): could not find function "grid.arrange"