loads a few functions I often need

all_ablines | Plot vertical, horizontal and diagonal ablines |

arrayplot | Show an image based on row/column information |

auc | shorthand to return the AUC calculated by pROC |

auc.pval | shorthand to return the the p-value of AUC calculated by pROC |

balanceset | Balance samples |

browse | Browse a large object |

calcDif | Create a "difference" gene expression set |

catf | Shortcut with sprintf |

cc | Smart counters for rmarkdown |

centers.predict | useful for predicting cluster membership from cmeans and... |

clustCompPlot | compare different clusters in an overview plot |

clustplot | first attempt at pca/clustering plot (not working?) |

clustsizes | calculate sizes of clusters |

combineTopTableAll | Convert a topTableAll results by gene ID |

confuMat | Calculate a confusion matrix |

copyan | Annotated PDF copy of the graph produced |

dfsearch | Search through a data frame |

ding | Show a zenity dialog "Calculation complete" |

distVI | Calculate the variation of information distances |

dmtx2graph | Convert a distance matrix to an undirected graph |

dotpair | A variant of the pairs plot |

factorsummary | Convert columns of a data.frame to factors and show summary |

fastboxplot | A boxplot consisting of lines only |

fig_label | Create a label at the top left of the graphics device |

genePairs | Pairs plot using smoothScatter |

getGOrilla | Wrapper to run the online GO service GOrilla |

getsubsets | Sample a number of samples by factor levels |

grep.df | Quick grep through all columns of a data frame |

likelihood.test | Likelihood test |

linepairs | Beeswarm with lines linking pairs |

lineq | Parameters of a line drawn on a plot |

lp | Send current graph to printer. |

mkdesign | Quickly make a design |

MSD | Calculate MSD based on logFC and CI |

mybarplot | A variant box and whiskers plot |

myfaces | Chernoff faces |

myfuncs-package | My collection of utility functions |

myfuncs.reload | Reload the myfuncs package |

mykfold | kfold cross-validation with additional features |

myloess.sd | Local Polynomial Regression Fitting with Variability bands |

myloo | leave one out cross-validation with additional functions |

mypalette | A nice, pastel color palette |

myPlotDensities | Alternative to plotDensities from the limma package. |

na.lomf | Last observation moved forward |

normtosel | Standarization using a subset of the data |

os | Report memory usage |

pairedLOO | RF LOO removing whole group of subjects |

pairedswarm | Beeswarm with lines linking pairs |

pca2var | Calculate the variance explained for prcomp objects |

pcaR2 | Calculate R-squared for a matrix or principal components |

pcaR2plot | Automatic R2 plot |

plotGenes | Simple function to plot gene expression |

plotMyloess | Plot an object from myloess.sd |

plotROCseries | Plot a series of ROCs |

prcomp2 | A wrapper around prcomp |

prconvert | Convert RF votes to plottable object |

pval2str | Convert a p-value to a character corresponding to p-value... |

qval2signedqval | Change q values to logarithmized signed q values |

repsapply | A more general version of avereps |

rf2pr | Convert random forest to format suitable for rocplot() |

rg2csv | Save an RG object as CSV files |

rocformat | Format AUC from roc() function |

rocplot | Calculate and show ROC curve |

rocseries_boxplot | plot a series of ROC prediction objects as boxplot |

rocseries_table | Return a table with AUC for each prediction in a series |

runSPIA | wrapper for the spia function. |

saveAsCLS | Write pheno data as braindead CLS format |

saveAsGCT | Write expression data in the braindead GCT format |

save.xlsx | Save multiple objects to an excel file |

sdbar | Draw whiskers on a plot |

setColnames | Return the object with colnames set |

setdiff | Set difference operator |

setEdgeAttr | set Edge attributes in an Rgraphviz graph |

shortcuts | Shortcuts for common functions |

show.color | Shows a rectangle colored by that color |

showgene | A combined beeswarm / boxplot |

showGraph | Call RCytoscape functions to display a graph |

simpleGOhyper | simple alternative to hyperGTest |

smoothPalette | Create a gradient corresponding to a numeric vector |

sortby | Shortcuts for sorting data frames |

topTableAll | Create a topTable for all coefficients in a limma fit object |

ttmake | Create a topTable for limma with "msd" based on confidence... |

ttplot | beeswarm for a top table (result of topTableAll) plot |

ttsummary | Print a summary of a top table. |

whatabout | Inteligently find significant coefficients for a gene |

xclip | Copy a few history lines to the X primary clipboard |

xpredict | Cross predict from one data set to another |

xpredict.nvar | Determine optimal number of variables |

zz | Save history and data image |

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