Oncoprint Graphs : General parameters for oncoprints

# oncoprintAlteredText

Flag to show the alteration frequency as text (e.g. 83%) to the right of each row in the oncoprint

Type: boolean

Default: true

Used in: Heatmap

# oncoprintCNA

String to identify the data object to use to draw the copy number alterations; that is the amplifications (which will be colored red) and deletions (which will be colored blue). It MUST be a file with only two categorical levels

Type: string

Default:

Used in: Heatmap

# oncoprintColSummary

Flag to show column summary in oncoprints

Type: boolean

Default: false

Used in: Heatmap

# oncoprintEXP

String to identify the data object to use to draw the mRNA expression call as a cell border (e.g. mRNA high, mRNA low). Drawn as a border so it does not compete with the copy-number background or mutation bar

Type: string

Default:

Used in: Heatmap

# oncoprintHeatmapPosition

Position for the heatmap in the oncoprint

Type: string

Default: bottom

Options: right, bottom, left, top

Used in: Heatmap

# oncoprintMUT

String to identify the data object to use to draw the mutations. For example missense, non-synonymous, truncating, etc. Each level will be colored in a shade of green

Type: string

Default:

Used in: Heatmap

# oncoprintNoAlterations

Flag to switch to show variables and samples without any alterations

Type: boolean

Default: true

Used in: Heatmap

# oncoprintPresorted

Flag marking the oncoprint data as already ordered (e.g. cBioPortal gene-frequency and sample-cascade order); the default oncoprint sort is skipped so that order is kept

Type: boolean

Default: false

Used in: Heatmap

# oncoprintRowSummary

Flag to show row summary in oncoprints

Type: boolean

Default: false

Used in: Heatmap

# showHeatmapOncoprint

Flag to show/hide the heatmap along with the oncoprint

Type: boolean

Default: false

Used in: Heatmap