bmtable Class Reference

Detailed Description

BioMarker Table.

This is old code that is still in use for its ability to draw the "Peak Location" plots

It was originally a class to facilitate biomarker comparison between different datasets/methods. It can draw the "grades" curves (e.g. loadings, p-values, feature frequency histograms) and Peak Location Plots thereof.

It needs a lot of setup to work, so it is probably better to use draw_loadings_pl.m instead. The classes vis_loadings and have an option to visualize loadings/grades vectors as "Peak Location" plots vis_log_grades

If want to use this class directly, use demo_bmtable.m as a template to perform the following settings:

1. Assign blocks, datasets, peakdetectors, arts, units, and data_hint (optional)
2. Setup the grid property
3. Call draw_pl() or draw_lines()

See also

draw_loadings_pl.m, demo_bmtable.m

Definition at line 22 of file bmtable.m.

Public Member Functions
function	bmtable ()
function	check_booted (in o)
function	boot (in o)
function	draw_lines (in o, in i_row)
function	draw_pl (in o, in flag_wntext, in flag_sig)
	Draws the Peak Locations (PL) plot. More...

Public Attributes
Property	grid
Property	datasets
Property	blocks
	Cell of block objects. More...
Property	peakdetectors
	Cell of peakdetector objects. More...
Property	arts
	Cell of bmart objects. More...
Property	units
	Cell of bmunit objects. More...
Property	sig_j
	Vector of indexes. As many elements as grid rows. Each element is the index of a grid column. More...
Property	sig_threshold
	Significance level. Maybe the granularity of this will change (doubt it). More...
Property	rowname_j
	Vector of indexes. As many elements as grid rows. Each element is the index of a grid column. More...
Property	rowname_type
	='dataset'. May be 'dataset' or 'block' More...
Property	colname_type
	='dataset'. May be 'dataset' or 'block' More...
Property	data_hint
	Used to draw the hint spectrum. More...
Property	linewidth
	=3.5 Width for lineas and markers. Note that this number will be actually multiplied by the global SCALE. More...
Property	flag_train
	=0. Whether or not to train the blocks More...

Protected Member Functions
function	draw_line (in o, in i, in j, in stuff)
function	draw_significance (in o, in cel, in yy)
function	shake_grid (in o)
function	calc_cols (in o)
function	make_legend (in o, in ll)
function	add_legend (in o, in i, in j, in ll)
	Checks if new (block, params) case is found; if not, adds case. More...
function	get_rowname (in o, in i)
function	get_initialblock (in o, in cel)
function	get_grades (in o, in cel)
function	get_grades_x (in o, in cel)
function	get_gradeslegend (in o, in cel)
	Grades legend for cell. More...

Protected Attributes
Property	rowdata
	Row-wise information. More...
Property	coldata
	Column-wise information. More...
Property	flag_reverse
	Whether the x-axis is reverse or not. More...
Property	flag_booted
Property	flag_data

Constructor & Destructor Documentation

function bmtable::bmtable

(

)

Member Function Documentation

function bmtable::add_legend ( in  o, in  i, in  j, in  ll  )

protected

Checks if new (block, params) case is found; if not, adds case.

function bmtable::boot

(

in

o

)

function bmtable::calc_cols ( in  o )

protected

Calculations before draw_lines()

First pass finds minima and maxima for each column across all rows. This will ensure that all draw_lines() (using one row only) will nevertheless use y-scales that will be the same for any row wich which draw_lines() is called.

Second pass will transfer the minima and maxima to absolute graphical coordinates, as I am not using subplots, but drawing the figure from scratch instead

function bmtable::check_booted

(

in

o

)

function bmtable::draw_line ( in  o, in  i, in  j, in  stuff  )

protected

Draws a line an updates 'stuff' structure. This structure contains yticks, yticklabels, handles for legends and legend texts

function bmtable::draw_lines	(	in	o,
		in	i_row
	)

Draws all the grades curves from one row of the grid

This function draws the grades for each item of one given row of the bmtable::grid. Each grade is drawn separately, creating a multi-panel figure; however, it does not use sub-plots; instead, it draws the whole figure from scratch in one single box-less plot area.

function bmtable::draw_pl	(	in	o,
		in	flag_wntext,
		in	flag_sig
	)

Draws the Peak Locations (PL) plot.

function bmtable::draw_significance ( in  o, in  cel, in  yy  )

protected

function bmtable::get_grades ( in  o, in  cel  )

protected

fcon_linear

Sensitive to "idx_fea"=1 and "flag_abs"=1 in params

function bmtable::get_grades_x ( in  o, in  cel  )

protected

function bmtable::get_gradeslegend ( in  o, in  cel  )

protected

Grades legend for cell.

Backwards, calls of get_L_fea_names(), then sequence of get_description calls

others: makes default with idx_fea and flag_abs

function bmtable::get_initialblock ( in  o, in  cel  )

protected

function bmtable::get_rowname ( in  o, in  i  )

protected

function bmtable::make_legend ( in  o, in  ll  )

protected

Makes legends: plots the markers then calls the legend() function passing the appropriate handles to it.

Currently used only by the PL plot. draw_lines() does not use it

function bmtable::shake_grid ( in  o )

protected

Empowers grid with calculated fields

grid.params

Grid cell parameters have defaults "idx_fea"=1 and "flag_abs"=1

Member Data Documentation

Property bmtable::arts

Cell of bmart objects.

Definition at line 48 of file bmtable.m.

Property bmtable::blocks

Cell of block objects.

Definition at line 42 of file bmtable.m.

Property bmtable::coldata

protected

Column-wise information.

Definition at line 86 of file bmtable.m.

Property bmtable::colname_type

='dataset'. May be 'dataset' or 'block'

Definition at line 66 of file bmtable.m.

Property bmtable::data_hint

Used to draw the hint spectrum.

Definition at line 69 of file bmtable.m.

Property bmtable::datasets

array of irdata.

datasets are used only if rowname_type is 'dataset'. They are used to get row names (will be dataset.title)

If not used, grid.i_dataset will be irrelevant.

Definition at line 39 of file bmtable.m.

Property bmtable::flag_booted

protected

Definition at line 95 of file bmtable.m.

Property bmtable::flag_data

protected

Definition at line 97 of file bmtable.m.

Property bmtable::flag_reverse

protected

Whether the x-axis is reverse or not.

Definition at line 89 of file bmtable.m.

Property bmtable::flag_train

=0. Whether or not to train the blocks

Definition at line 75 of file bmtable.m.

Property bmtable::grid

2D struct

i_block, i_dataset, i_peakdetector, i_art, i_unit point to elements in respective properties; flag_sig indicated whether to draw significance threshold line; params if passed to get_gradeslegend() and get_grades() (please note: post-training!); peakidxs, peak_y, y are calculated with shake_grid().

Definition at line 31 of file bmtable.m.

Property bmtable::linewidth

=3.5 Width for lineas and markers. Note that this number will be actually multiplied by the global SCALE.

Definition at line 72 of file bmtable.m.

Property bmtable::peakdetectors

Cell of peakdetector objects.

Definition at line 45 of file bmtable.m.

Property bmtable::rowdata

protected

Row-wise information.

Definition at line 83 of file bmtable.m.

Property bmtable::rowname_j

Vector of indexes. As many elements as grid rows. Each element is the index of a grid column.

Definition at line 60 of file bmtable.m.

Property bmtable::rowname_type

='dataset'. May be 'dataset' or 'block'

Definition at line 63 of file bmtable.m.

Property bmtable::sig_j

Vector of indexes. As many elements as grid rows. Each element is the index of a grid column.

Definition at line 54 of file bmtable.m.

Property bmtable::sig_threshold

Significance level. Maybe the granularity of this will change (doubt it).

Definition at line 57 of file bmtable.m.

Property bmtable::units

Cell of bmunit objects.

Definition at line 51 of file bmtable.m.

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The documentation for this class was generated from the following file:

• bmtable.m