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Chris Grace edited this page Nov 26, 2019 · 12 revisions

The Manhattan++ plot displays a heatmap that comprises cells which correspond to a chr:bp interval and a -log10 p-value interval. The heatmap displays the characteristics of these cells and the way this is achieved is specified in the configuration file.

For example below a cell which is defined as the variants with chr:bp between chr1:9,000,000 and chr1:12,000,000 (3Mb) and -log10 -pvalue between 15.875 (1.33E-16) and 16 (1.00E-16) (0.125). The configuration file determines how this cell is reported (for example the count of variants and the MAF of these variants)

zoom

The configuration controls the types of bins which are available in the heatmap and reported in the legend.

Each bin has the following characteristics:

  1. An unique index which is assigned to the bin in the heatmap
  2. A lower and upper bounds of the number of variants in the bin.
  3. A colour for the bin in the heatmap and the legend. (Must be in grDevices::colors())
  4. The type of the bin - val is a normal cell, oddchr and evenchr, specify the colours of the odd and even chromosomes below the FDR threshold.
  5. A flag to determine whether the bins should be labelled on the heatmap (with bubble)
  6. Does the bin report variants with MAF less than a certain threshold?
  7. Does the bin report variants with the consequence variable set to 1?

For example in the figure below:

  • Index number 5 reports cells which have between 2 and 400 variants, with no MAF below the threshold and with no variants which have the consequence flag.
  • Index number 6 has between 2 and 400 variants, but with at least one variant with the consequence flag and with no MAFs less than the threshold.
  • Index number 7 has between 2 and 400 variants, with at least one variant which is less than the MAF threshold and no variants with the consequence flag.
  • Index 8 has between 2 and 400 variants, with at least one variant with the consequence flag and at least on variant which has a MAF less than the threshold.

cells

Configuration file

To define the legend and type of heatmap cells.

  1. min.count - Lower bounds of number of variants in this cell
  2. max.count - Upper bounds of number of variants in this cell.
  3. maf - Should variants with minor allele frequencies below the threshold be detected by this cell?
  4. conseq - Should any HIGH consequence variant be detected?
  5. col - The colour of the heatmap cells
  6. idx - Index for labeling on the heatmap
  7. type - The type of cell: val or oddchr / evenchr
  8. report - Should these cells be reported on the heatmap with bubble label?

The variable configfile should be modfied to point to this file (with the file structure of the operating system used)

#### CONFIG file for use with MANH++ - Do not modify the first 10 lines							
## min.count: The lower cell count threshold to accept this config							
## max.count: The upper cell count threshold to accept this config							
## maf: Is MAF detection active for this config - is there any variants within a cell with MAF < threshold?	
## conseq: Is HIGH impact consequence active? Are there any variants with HIGH impact consequence in the cell?		
## col: The colour which cells for this config							
## idx: the index to use for this cell in the heatmap - MUST BE CONSECUTIVE FROM START TO END - STARTING AT 1
## type: val - an config entry, oddchr - the odd chromosome, evenchr - the even chromosome"		
## report: Are these annotations labeled on the heatmap							
#####		
min.count   max.count   maf     conseq    col         idx     type    report
1           1           FALSE   FALSE     black       1       val     FALSE
1           1           FALSE   TRUE      light pink  2       val     TRUE
1           1           TRUE    FALSE     green       3       val     FALSE

Also see the example file (config.txt) for more information.

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