Outputs

Getting PDFs and cluster info

Plots can be downladed as PDFs by clicking Line plot or Heatmap buttons in the "Download:" section of the tool panel (above the plot preview).

The small buttons next to Line plot and Heatmap produce additional output files:

• the i button next to Line plot downloads the PDF containing average plot keys
• cluster diagram button next to Heatmap downloads a cluster report giving cluster assignments and sorting order for each feature as a comma separated value (CSV) spreadsheet.

The cluster report contains following columns:

• chromosome - the name of chromosome, contig or scaffold
• start - start of the feature (1 based chromosomal coordinate)
• end - end of the feature (1 based chromosomal coordinate)
• width - width of the feature in base pairs
• strand - strand of the feature
• metadata_... - annotation columns present in the original GFF/BED e.g. gene name, score, group
• originalOrder - number of feature (row) in GFF/BED, can be used to restore original order after sorting on cluster ID
• ClusterID - the numeric ID of the cluster. The topmost cluster on the heatmap is annotated with 1, and the bottom cluster with k, where k equals to number of clusters selected, exported only if clustering is enabled
• SortingOrder - the order imposed on heatmap by sorting by mean row(s) values, exported only if sorting is enabled
• FinalOrder - the final order of heatmap's rows, this can be influenced by sorting and clustering; 1 indicates topmost row

Sample report: \footnotesize

chromosome	start	end		width	strand	metadata_group	originalOrder	ClusterID	SortingOrder	FinalOrder
chrI		9065087	9070286	5200	+		g1				1				1			3				3
chrI		5171285	5175522	4238	-		g1				2				3			50				43
chrI		9616508	9618109	1602	-		g1				3				3			13				43
chrI		3608395	3611844	3450	+		g1				4				3			11				12

\normalsize

Table view: \scriptsize

chromosome	start	end	width	strand	metadata_group	originalOrder	ClusterID	SortingOrder	FinalOrder
chrI	9065087	9070286	5200	+	g1	1	1	3	3
chrI	5171285	5175522	4238	-	g1	2	3	50	43
chrI	9616508	9618109	1602	-	g1	3	3	13	43
chrI	3608395	3611844	3450	+	g1	4	3	11	12

\normalsize

PDF output size

The last tab (Batch operation and setup) on the tool panel includes batch operations and various other settings including PDF output size. By default the output PDF will be A4 landscape. This can be changed using the drop-down list to following settings:

• user defined - this option reveals two numeric inputs that allows to set output PDF width and height. The values must be given in inches.
• Legal rotated - US Legal landscape: 14" by 8.5"
• A4 - A4 portrait: - 8.27" × 11.69"
• Letter - US Letter portrait: 8.5" × 11"
• Legal - US Legal portrait: 8.5" × 14"
• Executive - a.k.a Monarch paper: 7.25 × 10.5"