- Jiejun Shi (shij@tongji.edu.cn)
- R with following packages
- getopt
$ Rscript DepiMap.r -h
Usage: Rscript DepiMap.r [-[-help|h]] [-[-SampleMatrixes|s] <character>] [-[-SampleNames|n] <character>] [-[-Zmax|z] <character>] [-[-Colors|c] <character>] [-[-SmoothWindow|S] <integer>] [-[-Subtrahend|u] <character>] [-[-Minuend|m] <character>] [-[-DeltaZmax|Z] <character>] [-[-DeltaColors|C] <character>] [-[-IDfiles|i] <character>] [-[-IDorder|I]] [-[-WhichOrder|w] <character>] [-[-OrderInterval|v] <character>] [-[-Decreasing|d] <character>] [-[-DeltaOrder|o] <character>] [-[-LabelIDfile|l] <character>] [-[-ColorResolution|r] <integer>] [-[-UseRaster|R]] [-[-OutTiff|t] <character>] [-[-PanelWidth|W] <integer>] [-[-TotalHeight|H] <integer>] [-[-Xtick|x] <character>]
-h|--help useage
-s|--SampleMatrixes Sample matrixes seperated by ",". REQUIRED.
-n|--SampleNames Names list("," seperated) in the same length as SampleMatrixes. REQUIRED.
-z|--Zmax Zmax list("," seperated) in the length of either 1 or the same as SampleMatrixes. REQUIRED.
-c|--Colors Color list("," seperated) in the length of either 1 or the same as SampleMatrixes. Default is blue.
-S|--SmoothWindow Window size(number of matrix columns) used for Smoothing. Default is 1, i.e. no smoothing.
-u|--Subtrahend Sample Names("," seperated) which will be used as Subtrahend in Delta-Heatmaps.
-m|--Minuend Sample Name which will be used as Minuend in Delta-Heatmaps, only 1 Minuend sample supported.
-Z|--DeltaZmax Zmax of Delta-Heatmaps("," seperated) in the length of either 1 or the same as Subtrahend Samples. REQUIRED if Subtrahend and Minuend are detected.
-C|--DeltaColors 3 colors("," seperated)corresponding to -DeltaZmax,0,DeltaZmax in Delta-Heatmaps. Default is "black,white,orange".
-i|--IDfiles ID list files("," seperated). One ID each row. Only the rows in matrixes whose id(4th column) included are presented in heatmap. Multiple horizontal panels will presented if multiple ID files detected. If absent, all rows are presented.
-I|--IDorder Whether sort each horizontal panel by IDfiles.
-w|--WhichOrder Sample Names which will be used to order each horizontal panel. The length must be the same as IDfiles count. Default is the first Sample Name.
-v|--OrderInterval Two integers indicate the columns which are used to order matrix rows. If absent, all columns are used.
-d|--Decreasing List of 1 and/or 0 means whether order Decreasingly or not. The length must be the same as IDfiles count. Default is 1.
-o|--DeltaOrder List of 1 and/or 0 means whether order by Delta-Heatmap or Raw heatmap. The length must be the same as IDfiles count. The Delta-Heatmap must be plotted if you want to order by it. Default is 0.
-l|--LabelIDfile A file of IDs which will be labeled in heatmap. One ID each row.
-r|--ColorResolution Divide 1 into this number of colors. Default is 1.
-R|--UseRaster Whether useRaster for the heatmaps.
-t|--OutTiff Output tiff file name. Default is "Output_Heatmap.tiff".
-W|--PanelWidth Width of each Column Panel. Default is 300.
-H|--TotalHeight Total Height of the plot. Default is 1200.
-x|--Xtick Xtick interval length indicated by either 2(TSS upstream and downstream) or 3(TSS upstream, genebody and TES downstream) integers seperated by ",". Default is 5000,5000.
Note: deeptools-computeMatrix is recommended to generate the input SampleMatrix.
DepiMap was introduced and used in papers below.
Shi, J. et al. Drosophila Brahma complex remodels nucleosome organizations in multiple aspects. Nucleic Acids Research 42(15):9730-9739 (2014).
Hsu, C.C., Shi, J. et al. Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes & Development 32:58-69 (2018).