Description Usage Arguments Value Author(s) Examples
This function creates a heat map for a data set based on a univariate or frequency ranking
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variableList |
A data frame with two columns. The first one must have the names of the candidate variables and the other one the description of such variables |
varRank |
A data frame with the name of the variables in |
Outcome |
The name of the column in |
data |
A data frame where all variables are stored in different columns |
title |
The title of the plot |
hCluster |
Logical. If |
prediction |
A vector with a prediction for each subject, which will be used to rank the heat map |
Scale |
An optional value to force the data normalization |
theFiveColors |
the colors of the heatmap |
outcomeColors |
the colors of the outcome bar |
transpose |
transpose the heatmap |
... |
additional parameters for the heatmap.2 function |
dataMatrix |
A matrix with all the terms in |
orderMatrix |
A matrix similar to |
heatMap |
A list with the values returned by the |
Jose G. Tamez-Pena and Antonio Martinez-Torteya
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ## Not run:
library(rpart)
data(stagec)
# Set the options to keep the na
options(na.action='na.pass')
# create a model matrix with all the NA values imputed
stagecImputed <- as.data.frame(nearestNeighborImpute(model.matrix(~.,stagec)[,-1]))
# the simple heat map
hm <- heatMaps(Outcome="pgstat",data=stagecImputed,title="Heat Map",Scale=TRUE)
# transposing the heat-map with clustered colums
hm <- heatMaps(Outcome="pgstat",data=stagecImputed,title="Heat Map",Scale=TRUE,
transpose= TRUE,hCluster = TRUE,
cexRow=0.80,cexCol=0.50,srtCol=35)
# transposing the heat-map with reds and time to event as outcome
hm <- heatMaps(Outcome="pgtime",data=stagecImputed,title="Heat Map",Scale=TRUE,
theFiveColors=c("black","red","orange","yellow","white"),
cexRow=0.50,cexCol=0.80,srtCol=35)
## End(Not run)
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Loading required package: Rcpp
Loading required package: stringr
Loading required package: miscTools
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Attaching package: 'Hmisc'
The following objects are masked from 'package:base':
format.pval, units
Loading required package: pROC
Type 'citation("pROC")' for a citation.
Attaching package: 'pROC'
The following objects are masked from 'package:stats':
cov, smooth, var
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