A tool to plot metagene plots as well as metagene heatmaps for the gedi toolkit
To run MetagenePlot download the latest release and execute the following console command (with appropriate parameters):
java -cp MetagenePlot.jar -prefix <Prefix> -binSizes <binSizes> -binNames <binNames> -readData <reads>.cit -locFile <locafile>.tsv <Options>
An example call could look like this:
java -cp MetagenePlot.jar -prefix outputFolder -readData reads.cit -strandness SENSE -binSizes "100,10,500" -binNames "upstream,InterestingPosition,Downstream" -locFile locations.tsv -plot -readType DENSITY -normMode TOTAL -binNormMode MAX -readCountMode Weight -mergeConds "0,1/2/3"
The following options are available:
General:
-prefix <prefix> The prefix used for all output files
-binSizes <binSizes> The sizes of each bin comma separated (e.g.: 40,60,20 this creates three bins with a total of 3 bins)
-binNames <binNames> Comma separated string containing names for the bins. Need to be the same size (i.e. same amounts of commas as binSizes)
MetageneDataExtractor:
-readData <readData> Read data in CIT-format.
-locFile <locFile> File containing the locations to check for. The number of locations per line need to be the same as binSizes and binNames
[ -strandness <strandness> Strandness of the data (default: Sense) Choices are : AutoDetect,Sense,Antisense,Unspecific]
[ -mergeConds <mergeConds> Conditions to merge. Write as 0,2/1,3/4,5 to merge conditions 0 and 2, 1 and 3 and so on. (default: )]
[ -normMode <normMode> Normalization mode used for normalization (Total=sum over all readcounts, Maximum=Max readcount) (default: TOTAL) Choices are : TOTAL,MAXIMUM,NONE]
[ -totalRC <totalRC> Total read counts. Either nothing or same length as all conditions]
[ -readType <readType> Density, 3'- or 5'-end (default: DENSITY) Choices are : FIVE_PRIME,DENSITY,THREE_PRIME]
[ -readCountMode <readCountMode> mode of how to count reads (default: Weight)]
[ -binNormMode <binNormMode> Normalization mode used per bin (default: MEAN) Choices are : MEAN,MAX,SUM]
[ -useLog If values should be log10]
MetagenePlotter:
[ -plot Shall the R-plotting-script be run (needs RServ to be active)]
[ -noHeatmaps If plotting is enabled, heatmaps will be skipped (needs RServ to be active)]
[ -plotYMax <plotYMax> The max value for the y-axis (default: -1.0)]
[ -names <names> File containing the names for the genes in the locations file. Need to be in the same order!]
The locations-file provided by -locFile should be a text-file, where each row represents a location of interest and contains a number of genomic locations equal to the number of bins separated by tab stops.
A genomic location should look like this: <Chromosome><Strand>:<start>-<end>. An example for the location 1000 to 2000 on the plus strand of the chromosome 21 looks like the following: 21+:1000-2000. However, the same location on the negative strand of chromosome 21 looks like this: 21-:2000-1000, where the start and end points are reversed compared to the plus strand location. MetagenePlot always orients the 5'- and 3'-ends based on the start to end direction in the location string. This makes it possible, for example, to show the upstream antisense window in the first bin and the downstream sense window in the second bin. An example for this case would be the following line in the locFile: 21-:1000-2000 21+:2000-3000. Here the second bin show the location 2000 to 3000 on the plus strand in 5' to 3' direction. However, the first bin will show the location 1000 to 2000 on the minus strand from 3' to 5'.