| Type: | Package |
| Title: | Invasion Correction |
| Version: | 0.1 |
| Date: | 2017-02-20 |
| Author: | Marcus Rosenblatt |
| Maintainer: | Marcus Rosenblatt <marcus.rosenblatt@fdm.uni-freiburg.de> |
| Description: | The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube. The script fits a conical plane to give xyz-coordinates of the cells. It outputs the number of migrated cells and the new corrected coordinates. |
| License: | GPL-3 |
| Depends: | lattice, stats, utils |
| LazyData: | TRUE |
| RoxygenNote: | 5.0.1 |
| NeedsCompilation: | no |
| Packaged: | 2017-02-23 16:42:01 UTC; marcus |
| Repository: | CRAN |
| Date/Publication: | 2017-02-23 17:58:01 |
Correct invasion data by conical plane
Description
Correct z-component of a 3D collagen invasion essay. The correction is achieved under the assumption that non-migrating cells of the essay approximately form a quadratic flow profile due to frictional effects, compare law of Hagen-Poiseuille for flow in a tube.
Usage
correctByConicalPlane(filename, nrfits = 1000, threshold = -30,
plot = FALSE, write_csv = TRUE)
Arguments
filename |
Name of data file in csv format. It should contain columns "Pos_X", "Pos_Y" and "Pos_Z". |
nrfits |
Numeric, Number of randomly chosen starting points for the optimization. Choose lower values for speeding up computational time. Choose higher values for more reliable optimization results. |
threshold |
Numeric, A threshold for counting cells as being invaded or not. When cells move towards negative z-direction, threshold should be negative. |
plot |
Boole, if TRUE exemplary 3D plots before and after the correction are plotted |
write_csv |
if TRUE resulting corrected values are saved as a csv file |
Value
Data.frame containing input positions, corrected z-positions as well as number and percentage of invaded cells.
Author(s)
Marcus Rosenblatt, marcus.rosenblatt@fdm.uni-freiburg.de