/Heatmap-wrapper

Primary LanguageR

Heatmap-wrapper

Codes to generate heatmap, along with a example data set. Example to run the code (from command line):

Rscript HC.R PCA_example.csv T T T 5 T F Out.pdf

or

Rscript HC.R PCA_example.csv T T T 5 T F

or

Rscript HC.R PCA_example.csv T T T 5 T F Out.pdf NULL NULL F

or

Rscript HC.R PCA_example.csv T T T 5 T F Out.pdf NULL NULL F 3 10 15 8 T

or (To see heatmap by WaveCrestENI recovered cell order)

Rscript HC.R WC_example.csv T F T 5 T T Out.pdf NULL NULL

or (To see heatmap by WaveCrestENI recovered cell order)

Rscript HC.R WC_example.csv T F T 5 T T Out.pdf GeneList.csv Condition.csv

or (To see heatmap by WaveCrestENI recovered cell order)

Rscript HC.R WC_example.csv T F T 5 T T Out.pdf GeneList.csv Condition.csv T 3 10 15 8 T

The inputs for the code are:

  • [FileNameIn] can take .csv, .txt or .tab

  • [Whether cluster by rows T/F]

  • [Whether cluster by columns T/F]

  • [Whether scale data within a row T/F]

  • [Lower limit of detection] Genes with max expression below this threshold will be removed.

  • [Need normalization or not] If T is specified, median-by-ratio normalization will be performed prior to PCA analysis

  • [Whether run WaveCrest or not (RunWaveCrest)] If T is specified, WaveCrestENI will be performed prior and will plot heatmap by WaveCrestENI recovered cell order. If F is specified, regular heatmap will be provided, and both Condition.csv and markerList.csv files will be ignored

  • [OutputName] Need to be XX.pdf. The pdf width and height will be automatically adjusted based on # genes and # samples

  • [FileNameIn] can take .csv, .txt or .tab for WaveCrestENI (list of key markers) . If NULL and RunWaveCrest =T ,all genes will be used for WaveCrestENI.

  • [FileNameIn] can take .csv, .txt or .tab for WaveCrestENI (condition of cells). If NULL and RunWaveCrest=T,. all cells will be considered as single condition.

  • [X11 activation] Default is T. If it is specified as F, X11 will be disactived

  • [bottom margin] [right margin] Two numbers to define margin width. Default is 7 for both parameters.

  • [pdf height] [pdf width] Two numbers to define pdf height and width. Default height is #rows/5; default width is #column/4.

  • [color] Heatmap color scheme. Default is yellow and purple. If T, green and red will be applied.

If the last input is specified, the heatmap will be output as a pdf file. Otherwise it will be shown in console. yellow-green color scheme is used as default.