plotMethylationDataSpatialCorrelation: Plot methylation data spatial correlation
In nrzabet/DMRcaller: Differentially Methylated Regions caller

Description Usage Arguments Details Value Author(s) See Also Examples

This function plots the correlation of methylation levels for Cytosines located at a certain distance apart.

plotMethylationDataSpatialCorrelation(methylationData1,
  methylationData2 = NULL, distances, regions = NULL,
  conditionsNames = NULL, context = "CG", labels = NULL, col = NULL,
  pch = c(1, 0, 16, 2, 15, 17), lty = c(4, 1, 3, 2, 6, 5),
  contextPerRow = FALSE, log = "")

`methylationData1`	the methylation data in condition 1 (see `methylationDataList`).
`methylationData2`	the methylation data in condition 2 (see `methylationDataList`). This is optional.
`distances`	a `numeric` vector specifing the different values for the distances when computing the correlation.
`regions`	a `GRanges` object with the regions where to compute the correlation. If `NULL`, the coverage is computed genome-wide.
`conditionsNames`	a vector of character with the names of the conditions for `methylationData1` and `methylationData2`.
`context`	the context in which the DMRs are computed (`"CG"`, `"CHG"` or `"CHH"`).
`labels`	a `vector` of `character` used to add a subfigure character to the plot. If `NULL` nothing is added.
`col`	a `character` vector with the colors. It needs to contain a minimum of 2 colors per condition. If not or if `NULL`, the defalut colors will be used.
`pch`	the R symbols used to plot the data. It needs to contain a minimum of 2 symbols per condition. If not or if `NULL`, the defalut symbols will be used.
`lty`	the line types used to plot the data. It needs to contain a minimum of 2 line types per condition. If not or if `NULL`, the defalut line types will be used.
`contextPerRow`	a `logical` value indicating if the each row represents an individual context. If `FALSE`, each column will represent an individual context.
`log`	a `character` indicating if any of the axes will be displayed on log scale. This argument will be passed to `plot` function.

This function plots the proportion of cytosines in a specific context that have at least a certain number of reads (x-axis)

Invisibly returns NULL

Nicolae Radu Zabet

computeMethylationDataSpatialCorrelation, methylationDataList

## Not run: 
# load the methylation data
data(methylationDataList)

# plot the spatial correlation in CG context
par(mar=c(4, 4, 3, 1)+0.1)
plotMethylationDataSpatialCorrelation(methylationDataList[["WT"]],
                           distances = c(1,5,10,15), regions = NULL,
                           conditionsNames = c("WT","met1-3"),
                           context = c("CG"),
                           labels = LETTERS, col = NULL,
                           pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5),
                           contextPerRow = FALSE)

# plot the spatial correlation in all three contexts
plotMethylationDataSpatialCorrelation(methylationDataList[["WT"]],
                           methylationDataList[["met1-3"]],
                           distances = c(1,5,10,15,20,50,100,150,200,500,1000),
                           regions = NULL, conditionsNames = c("WT","met1-3"),
                           context = c("CG", "CHG", "CHH"),
                           labels = LETTERS, col = NULL,
                           pch = c(1,0,16,2,15,17), lty = c(4,1,3,2,6,5),
                           contextPerRow = FALSE, log="x")

## End(Not run)