The table editor will automatically calculate these statistics for each sample in the group. Only drag statistics from a single sample into the
Group: remember to click on the appropriate group in the workspace window before you create the table! The table is created for those samples in the currently-selected In the drop-down menu shown at the right, in the Table Editor.Įach statistic in the right panel of the table editor will correspond to a column in the output table you can change the order of these columns by clicking and dragging the statistics around. You can change the default choice there or Limnology and Oceanography 42, 874–880.When you drag a population node into the table editor, it assumes that you want the statistic that is set as your default in the Preferences on the Tables/Layouts tab. Cytometric diversity in marine ultraphytoplankton. Wanderley, Maria Victoria Quiroga, Andre M. Argument to be passed to vegan::metaMDS function.Ī list containing alpha index, beta matrix and Pielou's indices for each cytogram.īruno M.S. If TRUE, Hellinger transformation is applyed to data before analysis.ĭimensions of plot devices, in centimeters. The beads gate should be named exactly the same in all samples from the workspaces. Necessary only if use.beads is set to “TRUE”. Name of the gate describing the standard region to be used (usually bead's regions). It is recommended to proceed this way only if samples were analyzed with different settings. If “TRUE”, it centers all cytograms under a common point, based on the arithmetic mean of a standard region for all cytograms (usually beads regions), before proceeding to analysis. Maximum estimated p value for displayed variables on NMDS plot, as required by vegan::plot.envifitĮnviromental matrix associated to the set of cytograms under analysis. By default, it is assumed that all samples have no dilutions whatsoever (i.e. Its lenght is the same as the total number of samples meant to be analyzed and must follow the exact same order in which samples are presented to the function (the order of samples corresponds both to the order of workspace described in "myworkspaces" parameter and their order in each of these FlowJo workspaces). If TRUE, one must set minimum and maximum range for each channel individually.Ī vector containing dilution factors for each sample in the workspaces. It plots scatterplots of gated populations and displays grid lines corresponding to the limits of the bins. Should be one of the sixteeen avaiable for vegan::vegdist function. Method used to calculate beta diversity index of cytograms.
Should be one of "shannon", "simpson" or "invsimpson", as for vegan::diversity function. the degree of similarity between two cytograms). Method used to calculate alpha diversity index of cytograms (i.e. The gate should be named exactly the same in all samples from the workspaces. fcs files (versions 2.0 or 3.0) with its original names. More than one workspace can be analyzed at the same time. FlowDiv ( myworkspaces, gate.name = NULL, ialpha = "invsimpson", ibeta = "bray", do.plot = FALSE, static = FALSE, dilutions = NULL, pmax = 0.05, env = NULL, use.beads = FALSE, beads = NULL, transform.hell = FALSE, dimension = 20, psize = 3, autotrans = FALSE )Ī list containing the paths to FlowJo workspaces or GatingSet which are meant to be analyzed.
0 kommentar(er)
