plotCor {ChIPSeqSpike} | R Documentation

## Plot the correlation between ChIP-seq experiments

### Description

Plot the correlation between ChIP-seq experiments using heatscatter plot or, if heatscatterplot = FALSE, correlation tables.

### Usage

      plotCor(theObject, rawFile = FALSE, rpmFile = FALSE, bgsubFile = FALSE,
    revFile = FALSE, spiked = TRUE, main = "", add_contour = FALSE, method_cor =
    "spearman", nlevels = 10, color_contour = "black", show_cor = TRUE,
    allOnPanel = TRUE, method_scale = "none", method_corrplot = "circle",
    heatscatterplot = TRUE, type_corrplot = "upper", diag_corrplot = FALSE,
    separateWindows = FALSE, verbose = FALSE, ...)

    ## S4 method for signature 'ChIPSeqSpikeDataset'
    plotCor(theObject, rawFile = FALSE, rpmFile =
    FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE, main = "",
    add_contour = FALSE, method_cor = "spearman", nlevels = 10, color_contour =
    "black", show_cor = TRUE, allOnPanel = TRUE, method_scale = "none",
    method_corrplot = "circle", heatscatterplot = TRUE, type_corrplot = "upper",
    diag_corrplot = FALSE, separateWindows = FALSE, verbose = FALSE, ...)

    ## S4 method for signature 'ChIPSeqSpikeDatasetBoost'
    plotCor(theObject, rawFile = FALSE,
    rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE, main = "",
    add_contour = FALSE, method_cor = "spearman", nlevels = 10,
    color_contour = "black", show_cor = TRUE, allOnPanel = TRUE, method_scale =
    "none", method_corrplot = "circle", heatscatterplot = TRUE, type_corrplot =
    "upper", diag_corrplot = FALSE, separateWindows = FALSE, verbose = FALSE, ...)

    ## S4 method for signature 'ChIPSeqSpikeDatasetList'
    plotCor(theObject, rawFile = FALSE, rpmFile
    = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE, main = "",
    add_contour = FALSE, method_cor = "spearman", nlevels = 10, color_contour =
    "black", show_cor = TRUE, allOnPanel = TRUE, method_scale = "none",
     method_corrplot = "circle", heatscatterplot = TRUE, type_corrplot = "upper",
     diag_corrplot = FALSE, separateWindows = FALSE, verbose = FALSE, ...)

    ## S4 method for signature 'ChIPSeqSpikeDatasetListBoost'
    plotCor(theObject, rawFile = FALSE,
    rpmFile = FALSE, bgsubFile = FALSE, revFile = FALSE, spiked = TRUE, main = "",
    add_contour = FALSE, method_cor = "spearman", nlevels = 10,
    color_contour = "black", show_cor = TRUE, allOnPanel = TRUE,
    method_scale = "none", method_corrplot = "circle", heatscatterplot = TRUE,
    type_corrplot = "upper", diag_corrplot = FALSE, separateWindows = FALSE,
    verbose = FALSE, ...)

### Arguments

`theObject` | `ChIPSeqSpike` dataset (see ?spikeDataset)
`rawFile` | If TRUE, use the untransformed data. Not available in boost mode. Default is FALSE. (see details)
`rpmFile` | If TRUE, use the RPM scaled data. Not available in boost mode. Default is FALSE. (see details)
`bgsubFile` | If TRUE, use the input subtracted data. Not available in boost mode. Default is FALSE. (see details)
`revFile` | If TRUE, use the RPM reverted data. Not available in boost mode. Default is FALSE. (see details)
`spiked` | If TRUE, use the spiked data. Default is TRUE. (see details)
`main` | Main title of the plot. No title is displayed by default.
`add_contour` | If TRUE, contours are added to the heatscatter. Default is FALSE.
`method_cor` | A character string indicating which correlation coefficient is to be computed. One of 'pearson' (default) , 'kendall' or 'spearman'.
`nlevels` | An integer giving the number of levels of the contour lines. Not used if heatscatteplot is FALSE. Default is 10
`color_contour` | Character string defining the color of the contour line. Not used if heatscatteplot is FALSE. Default is 'black'.
`show_cor` | Logical indicating if the correlation is added to the title. Not used if heatscatteplot is FALSE. Default is TRUE.
`allOnPanel` | Logical indicating if all correlations should be on the same panel. Not used if heatscatteplot is FALSE. Default is TRUE.
`method_scale` | Character string indicating the scaling to be applied to the data. Possible values are 'none', 'log', 'asinh', 'cuberoot' or 'zscore'. Not used if heatscatteplot is FALSE.
`method_corrplot` | If heatscatterplot is FALSE, define the graphical representation used for the correlation table. Possible values are 'circle', 'square', 'ellipse', 'number', 'pie', 'shade' and 'color'. See ?corrplot::corrplot for more details. Default is 'circle'.
`heatscatterplot` | If TRUE, use a heatscatter representation instead of correlation table. see ?LSD::heatscatter for more details. Default is TRUE.
`type_corrplot` | If heatscatter is FALSE, define if the full ('full'), the lower triangular ('lower') or upper triangular matrix is displayed. Default is 'upper'.
`diag_corrplot` | If heatscatter is FALSE, logical indicating if the correlation coefficients are displayed on the principal diagonal. Default is FALSE.
`separateWindows` | If heatscatterplot is TRUE, Logical indicating if each plot is output to a separate window. Default is FALSE.
`verbose` | Logical indicating if processing messages are displayed. Default is FALSE
`...` | Additional parameter to pass to the LSD::heatscatter or corrplot::corrplot functions.

### Details

The 'rawFile', 'rpmFile', 'bgsubFile', 'revFile', 'spiked' parameters indicate if the untransformed, RPM scaled, input DNA subtracted, RPM reversed or spiked data should be used plotted. This option is only available if not in boost mode (see ?spikePipe for details on what these steps are).

### Value

If heatscatterplot is FALSE, return the correlation matrix.

### Methods (by class)

- `ChIPSeqSpikeDataset`: Method for signature theObject= 'ChIPSeqSpikeDataset'

- `ChIPSeqSpikeDatasetBoost`: Method for signature theObject= 'ChIPSeqSpikeDatasetBoost'

- `ChIPSeqSpikeDatasetList`: Method for signature theObject= 'ChIPSeqSpikeDatasetList'

- `ChIPSeqSpikeDatasetListBoost`: Method for signature theObject= 'ChIPSeqSpikeDatasetListBoost'

### Author(s)

Nicolas Descostes

### See Also

`spikeDataset` `heatscatter` `corrplot` `spikePipe` `plotTransform` `boxplotSpike` `plotHeatmaps` `plotProfile`

### Examples

    ## Sub-sample
    data("result_extractBinding")

    ## Heatscatter of spiked data using Spearman correlation
    plotCor(csds)

    ## Pearson correlation of log transformed raw data
    plotCor(csds,  rawFile = TRUE, spiked = FALSE,  main = "heatscatter",
    method_cor = "pearson", method_scale = "log")

    ## Correlation table of all transformation steps with circle representation
    plotCor(csds, rawFile = TRUE, rpmFile = TRUE, bgsubFile = TRUE, revFile = TRUE,
     spiked = TRUE, heatscatterplot = FALSE, verbose = TRUE)

    ## Correlation table of all transformation steps with number representation
    plotCor(csds, rawFile = TRUE, rpmFile = TRUE, bgsubFile = TRUE, revFile = TRUE,
     spiked = TRUE, heatscatterplot = FALSE, verbose = TRUE, method_corrplot =
     "number")

[Package ChIPSeqSpike version 1.4.0 Index]