SinaPlot: an enhanced chart for simple and truthful representation of single observations over multiple classes

Recent developments in data driven science, in particular computational biology, have led scientists to integrate data from several sources, over diverse experimental procedures, or databases. This alone poses a major challenge in truthfully visualising data, especially when the amount of data points varies between classes. To aid the presentation of datasets with differing sample size we have developed a new type of plot overcoming limitations of current standard visualization charts. Plots like bar charts, violin plots, strip charts or box-and-whiskers plots may provide visual information about mean/median, variance of the data, number of data points or density distribution of data; still, only a combination of these plots may provide all relevant information. We have designed a new and simple plot inspired by the strip chart and the violin plot that operates by letting the normalized density of points restrict the jitter along the x-axis. Τhe plot displays the same contour as a violin plot, but resembles a simple strip chart for small number of data points. In this way the plot conveys information of both the number of data points, the density distribution, outliers and data spread in a very simple, comprehensible and condensed format. The package for producing the plots is available for R through the CRAN network (https://cran.r-project.org/web/packages/sinaplot/index.html). In order to aid users without experience in R we also provide access to a web-server accepting excel sheets to produce the plots (http://servers.binf.ku.dk:8890/sinaplot/) .

A simple and low-cost solution for the automation of X-ray powder diffractometers with chart recorder output

X-ray powder diffraction is an established method for the qualitative identification of crystalline materials and their quantitative analysis. The new generation of X-ray diffraction systems are based on expensive digital/embedded control technology and computer interfaces. Yet many laboratories use conventional manual-controlled systems withXYstrip-chart recorders. Since the output spectrum is a strip chart (hard copy), raw data, essential for structural and qualitative analysis, are not readily available for further analysis. Upgrading to modern computerized diffractometers is very expensive. The proposed automation design described here is intended to enable the conventional diffractometer user to collect, store and analyze data quickly. The design also improves the resolution by five times compared with the conventional setup. For the automation, a PC add-on card has been designed to control and collect the timing and intensity counts from the conventional X-ray diffractometer, and suitable software has been developed to collect, process and present the X-ray diffraction data for both qualitative and quantitative analysis. Moreover, a major advantage of this design is that it does not warrant any physical modification of the hardware of the conventional setup; it is simply an extension to enhance the performance of collecting raw data with a higher resolution at desired intervals/timings.

MATCHDB - A Program for the Identification of Phases Using a Digitized Diffraction-Pattern Database

The availability of automated powder diffractometers, APD, has revolutionized the collection of diffraction data and allowed many improvements in the analysis of these data. The biggest change is the ease of digitizing the diffraction trace rather than preparing it as a strip chart on paper from an analog recorder. When the data are collected properly, the trace is a digitized record of intensity versus 2θ. The trace is an accurate representation of the diffraction pattern containing the sample information along with the spectral and instrument aberrations.

Subsurface fracture surveys using a borehole television camera and acoustic televiewer

Borehole television survey and acoustic televiewer logging provide rapid, cost-effective, and accurate methods of surveying fractures and their characteristics within boreholes varying in diameter from 7.6 to 15.3 cm. In the television survey, a camera probe is used to inspect the borehole walls. Measurements of location, orientation, infilling width, and aperture of fractures are made on the television screen and recorded on computer data record sheets. All observations are recorded on video cassette tapes. With the acoustic televiewer, oriented images of fractures in the borehole walls are recorded on a strip–chart log and also on video cassette tapes. The images are displayed as if the walls were split vertically along magnetic north and spread out horizontally. Measurements of fracture characteristics are made on the strip–chart log, using a digitizing table and a microcomputer, and the data recorded on floppy diskettes. In both surveys, an inclined fracture is displayed as a sinusoidal curve, from which the apparent orientation of the fracture can be measured. Once the borehole orientation is known, the true orientation of the fracture can be computed from its apparent orientation. Computer analysis of the fracture data, provides a rapid assessment of fracture occurrence, fracture aperture, and statistically significant concentrations of fracture orientations. Key words: borehole, television survey, acoustic televiewer logging, fractures, distribution, orientation, aperture.