inst/seqplots/www/help/Outputs.md

In Przemol/seqplots: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps

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"

Przemol/seqplots documentation built on May 14, 2022, 6:47 a.m.