Fine-tune which samples are plotted. Every variable chosen on the
Select
tab appears here automatically; add any other variable with
Filter columns
. Each histogram shows the samples passing all the
other
filters, with this variable's own selection highlighted.
Cohort and the Exclude checkboxes on the Select tab decide which samples are shown here at all.
Filters take effect on the plot when you press
Plot
.
Fiddly Options
Sizes are real ggplot values (font sizes in points). A size of 0 removes that item.
The green line under each name is what ggplot calls the setting.
More ggplot settings
Search every other ggplot setting: all theme elements (axis text angle, legend position,
grid lines, backgrounds, spacing ...) and the drawing settings of points, boxplots and the fit line.
Each one you pick appears below with its current default; choose from the menu, or type your own number or #hex colour.
A figure for a paper or a slide: choose its real size and resolution, adjust until the
preview reads well, then press
Plot
to download the file. The preview is the figure itself,
drawn at the size you asked for. These settings are separate from the Appearance tab:
sizes that suit the screen do not suit a 3.5 inch figure.
Sizes at final print size
You have removed the source line.
That is fine, but please cite T2 in any
publication or presentation that uses this figure:
The source line, and the citation for T2:
T2 Database and Search Tool, Nathan O. Siemers, Ph.D., https://www.fiveprime.orgcopy
T2 is a database and plotting tool for large tumor-profiling compendia:
the TCGA Pan-Cancer 2018 release and companion datasets. Every measurement
(expression, mutation, copy number, signatures, clinical annotation, survival)
is stored per sample, so any variable can be plotted against any other.
Select
: choose the data set, the variables to plot (X, Y, color, size,
one graph per category) and the cohort(s); then press Plot.
Plot
: the resulting graph, a summary of the samples behind it,
and a download of the plotted table.
Filter
: interactive histograms and sliders/checkboxes for every selected
variable (and any others you add) to fine-tune which samples are plotted.
Appearance
: point size, transparency, label sizes, multi-graph layout,
fit line and survival-plot options, and a search over every other ggplot setting.
Publish
: the current plot as a figure of a chosen physical size and
resolution (PNG, TIFF or PDF), with a live preview.
Citing T2:
T2 Database and Search Tool, Nathan O. Siemers, Ph.D., https://www.fiveprime.org