For beginning users to be able to play around with the plotting functions of BactMAP, I saved three example datasets in in a folder you can download here. These sets are the ssbB-set(kindly donated by my colleague Arnau), the dnaX/ftsZ-set and the ‘Van-FL dataset’. Below you can find the documentation:

The ssbB-set

Description

Dataset retrieved from movie previously published in Moreno-Gamez et al., 2017 (pubMED). Competence is induced with CSP, leading to expression of ssbB-GFP. The timing between cells differs slightly. I used SuperSegger to track the cells in the original movie. After this, I used BactMAP to extract the phylogeny. See the tutorial on genealogy to see the ssbB-set in action.

ssbB_meanfluo

Usage

load("ssbB_meanfluo.rda")

Format

A data frame with the following columns:

Column Name	Description
`node`	the number of the node in the genealogy tree
`birth`	birthframe of this cell
`cell`	cell identifier. unique per frame.
`death`	death frame (or frame the cell divides) of this cell
`edgelength`	the time (in frames) of the cell division
`fluorsum`	the sum of the total fluorescence inside the cell. inherited from SuperSegger (`'fluor sum'`, see the SuperSegger Wiki)
`fluormean`	the mean of the total fluorescence inside the cell. inherited from SuperSegger (`'fluor mean'`, see the SuperSegger Wiki)
`fluorsum_D`	the sum of the fluorescence at cell division . inherited from SuperSegger (`'fluor sum death'`, see the SuperSegger Wiki)
`fluormean_D`	the mean of the total fluorescence at cell division. inherited from SuperSegger (`'fluor mean death'`, see the SuperSegger Wiki)
`parent`	the node of the parent of this cell
`child1`	the cell number of the daughter cell of this cell
`child2`	the cell number of the other daughter cell of this cell
`root`	the root of the genealogy tree. by default, this is 0.
`nodelabel`	the cell number corresponding to the node

Source

Moreno-Gámez, Stefany, et al. “Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence.” Nature communications 8.1 (2017): 854.

Example

summary(ssbB_meanfluo)

##       node             cell           birth           death     
##  Min.   :  1.00   Min.   :  1.0   Min.   : 1.00   Min.   : 1.0  
##  1st Qu.: 50.00   1st Qu.: 50.0   1st Qu.:17.00   1st Qu.:26.0  
##  Median : 99.00   Median : 99.0   Median :25.00   Median :39.0  
##  Mean   : 99.48   Mean   :100.5   Mean   :24.57   Mean   :32.5  
##  3rd Qu.:149.00   3rd Qu.:150.0   3rd Qu.:36.00   3rd Qu.:40.0  
##  Max.   :198.00   Max.   :207.0   Max.   :40.00   Max.   :40.0  
##                                                                 
##    edgelength        fluorsum        fluormean        fluorsum_D     
##  Min.   : 0.000   Min.   : 47218   Min.   : 457.5   Min.   :  95546  
##  1st Qu.: 3.000   1st Qu.: 65794   1st Qu.: 466.2   1st Qu.: 152536  
##  Median : 8.000   Median : 81324   Median : 470.8   Median : 340060  
##  Mean   : 7.924   Mean   :151942   Mean   : 764.9   Mean   : 354852  
##  3rd Qu.:12.000   3rd Qu.:254545   3rd Qu.:1133.5   3rd Qu.: 460037  
##  Max.   :31.000   Max.   :492453   Max.   :1886.3   Max.   :1465046  
##                                                                      
##   fluormean_D         parent          child1          child2     
##  Min.   : 459.3   Min.   :104.0   Min.   : 10.0   Min.   : 11.0  
##  1st Qu.: 471.3   1st Qu.:125.0   1st Qu.: 56.5   1st Qu.: 57.5  
##  Median :1114.5   Median :149.0   Median :103.0   Median :104.0  
##  Mean   :1045.4   Mean   :149.3   Mean   :104.6   Mean   :105.6  
##  3rd Qu.:1379.1   3rd Qu.:174.0   3rd Qu.:151.5   3rd Qu.:152.5  
##  Max.   :2075.6   Max.   :198.0   Max.   :206.0   Max.   :207.0  
##                                   NA's   :103     NA's   :103    
##       root     nodelabel     
##  Min.   :0   Min.   :  0.00  
##  1st Qu.:0   1st Qu.: 21.00  
##  Median :0   Median : 48.00  
##  Mean   :0   Mean   : 50.74  
##  3rd Qu.:0   3rd Qu.: 78.00  
##  Max.   :0   Max.   :127.00  
##

ssbB_phylos

Usage

load("ssbB_phylos.rda")

Format

A phylo object containing the genealogy information of this timelapse movie: phylogenetic tree with 103 tips and 95 internal nodes.

Source

Moreno-Gámez, Stefany, et al. “Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence.” Nature communications 8.1 (2017): 854.

Example

summary(bactMAP::ssbB_phylos)

##             Length Class  Mode     
## edge        394    -none- numeric  
## tip.label   103    -none- character
## Nnode         1    -none- numeric  
## root.label    1    -none- character
## node.label   95    -none- character
## edge.length 197    -none- numeric  
## root.edge     1    -none- numeric

ssbB_network

Usage

load("ssbB_network.rda")

Format

iGRAPH network dataset containing the same information as ssbB_phylos & ssbB_meanfluo together

Source

Moreno-Gámez, Stefany, et al. “Quorum sensing integrates environmental cues, cell density and cell history to control bacterial competence.” Nature communications 8.1 (2017): 854.

Examples

#requires("igraph")

library(igraph)

##
## Attaching package: 'igraph'

## The following objects are masked from 'package:stats':
##
##     decompose, spectrum

## The following object is masked from 'package:base':
##
##     union

summary(ssbB_network)

## IGRAPH 431b225 DN-- 198 197 --
## + attr: name (v/c), birth (e/n), death (e/n), edgelength (e/n),
## | fluorsum (e/n), fluormean (e/n), fluorsum_D (e/n), fluormean_D
## | (e/n), child1 (e/n), child2 (e/n)

plot(ssbB_network)

The DnaX/FtsZ-set

Description

This short timelapse movie was taken for van Raaphorst, Kjos & Veening, 2017. I recently re-analyzed this dataset and saved the cell meshes, tracked DnaX & FtsZ filaments separately. I also saved the output of extr_OriginalCells() of the TIFF data of the FtsZ channel combined with the cell meshes of cell 4. If you want to play with the original data (TIFF files, Oufti and ISBatch output), click here. If you want to see the data in action, go to the tutorial on time-lapse data.

DnaX_mesh

Cell meshes, retreived by importing Oufti segmentation output in BactMAP using extr_Oufti().

Usage

load("DnaX_mesh.rda")

Format

A data frame with the following columns:

Column Name	Description
`X`	x-coordinate of cell outline point (pixels)
`Y`	y-coordinate of cell outline point (pixels)
`cell`	cell identifier. unique per frame.
`frame`	frame identifier. in this case, an image was taken every 20 seconds, so 1 frame corresponds to 20s.
`num`	number indicating the order of cell outline points (useful for plotting polygons)
`max.width`	maximum cell width in pixels
`length`	the point of cell length from pole 0
`steplength`	the distance (over the length axis) of this cell outline point from the previous cell outline point
`max.length`	the maximum cell length of the given cell
`xy`	indicates whether it’s the right or the left side of the cell (inherited from oufti)
`area`	cell area in pixels^2
`angle`	the angle of the cells length axis to the horizontal line of the image.
`Xmid`	the mid-point (pixel x-coordinate) of the cell
`Ymid`	the mid-point (pixel y-coordinate) of the cell
`X_rot`	the x-coordinate of the cell outline point (in pixels) when the cell length axis is horizontal, with mid-cell at (0,0)
`Y_rot`	the y-coordinate of the cell outline point (in pixels) when the cell length axis is horizontal, with mid-cell at (0,0)
`max_um`	the maximum cell length in micron
`maxwum`	the maximum cell width in micron
`Xrot_micron`	the x-coordinate of the cell outline point (in micron) when the cell length axis is horizontal, with mid-cell at (0,0)
`Yrot_micron`	the y-coordinate of the cell outline point (in micron) when the cell lenth axis is horizontal, with mid-cell at (0,0)

Source

van Raaphorst, Renske, Morten Kjos, and Jan-Willem Veening. “Chromosome segregation drives division site selection in Streptococcus pneumoniae.” Proceedings of the National Academy of Sciences 114.29 (2017): E5959-E5968.

Example

summary(DnaX_mesh)

##        X                Y               cell           frame       
##  Min.   : 28.25   Min.   : 67.88   Min.   : 1.00   Min.   :  1.00  
##  1st Qu.: 91.25   1st Qu.:108.13   1st Qu.: 9.00   1st Qu.: 49.00  
##  Median :127.09   Median :128.23   Median :16.00   Median : 94.00  
##  Mean   :129.44   Mean   :127.51   Mean   :18.14   Mean   : 93.32  
##  3rd Qu.:167.75   3rd Qu.:146.84   3rd Qu.:22.00   3rd Qu.:138.00  
##  Max.   :233.65   Max.   :183.22   Max.   :46.00   Max.   :181.00  
##       num          max.width         length         steplength     
##  Min.   : 0.00   Min.   :10.83   Min.   : 0.000   Min.   :-0.9323  
##  1st Qu.:13.00   1st Qu.:13.09   1st Qu.: 7.041   1st Qu.: 0.9216  
##  Median :27.00   Median :13.74   Median :13.886   Median : 1.0025  
##  Mean   :28.02   Mean   :13.74   Mean   :14.583   Mean   : 1.0249  
##  3rd Qu.:41.00   3rd Qu.:14.48   3rd Qu.:21.190   3rd Qu.: 1.1330  
##  Max.   :85.00   Max.   :15.58   Max.   :45.955   Max.   : 5.6841  
##    max.length          xy           area           angle          
##  Min.   :10.85   Min.   :0.0   Min.   :121.7   Min.   :0.0000198  
##  1st Qu.:24.94   1st Qu.:0.0   1st Qu.:238.5   1st Qu.:1.1230295  
##  Median :29.76   Median :0.5   Median :287.1   Median :1.6312324  
##  Mean   :29.22   Mean   :0.5   Mean   :289.4   Mean   :1.7271795  
##  3rd Qu.:33.51   3rd Qu.:1.0   3rd Qu.:332.3   3rd Qu.:2.3366826  
##  Max.   :45.96   Max.   :1.0   Max.   :486.1   Max.   :3.1399158  
##       Xmid             Ymid            X_rot           
##  Min.   : 40.87   Min.   : 80.33   Min.   :-20.194841  
##  1st Qu.: 90.81   1st Qu.:112.39   1st Qu.: -6.773118  
##  Median :127.98   Median :125.13   Median :  0.009878  
##  Mean   :129.48   Mean   :127.52   Mean   :  0.006536  
##  3rd Qu.:173.38   3rd Qu.:144.25   3rd Qu.:  6.779854  
##  Max.   :225.79   Max.   :173.85   Max.   : 20.194841  
##      Y_rot               max_um           maxwum      
##  Min.   :-8.699684   Min.   :0.7001   Min.   :0.6993  
##  1st Qu.:-5.892610   1st Qu.:1.6101   1st Qu.:0.8450  
##  Median :-0.032674   Median :1.9211   Median :0.8871  
##  Mean   : 0.002581   Mean   :1.8861   Mean   :0.8872  
##  3rd Qu.: 5.931830   3rd Qu.:2.1631   3rd Qu.:0.9344  
##  Max.   : 8.699684   Max.   :2.9664   Max.   :1.0057  
##      Xrot_micron               Yrot_micron          
##  Min.   :-1.3035770   Min.   :-0.5615646  
##  1st Qu.:-0.4372048   1st Qu.:-0.3803680  
##  Median : 0.0006377   Median :-0.0021091  
##  Mean   : 0.0004219   Mean   : 0.0001666  
##  3rd Qu.: 0.4376396   3rd Qu.: 0.3828996  
##  Max.   : 1.3035770   Max.   : 0.5615646

DnaX_tracks & FtsZ_tracks

Spot trajectories of DnaX and FtsZ filaments in a time-lapse, retrieved by importing ISBatch output using extr_ISBatch().

Usage

load("DnaX_tracks.rda")
load("FtsZ_tracks.rda")

Format

Both DnaX_tracks & FtsZ_tracks are data frames with the following columns:

Column Name	Description
`x`	x-coordinate of detected DnaX/FtsZ spot
`y`	y-coordinate of detected DnaX/FtsZ spot
`cell`	cell identifier. unique per frame.
`frame`	frame identifier. in this case, an image was taken every 20 seconds, so 1 frame corresponds to 20s.
`max.width`	maximum cell width in pixels
`max.length`	the maximum cell length of the given cell
`l`	relative localization of DnaX on the length axis of the cell.
`d`	relative localization of DnaX on the width axis (diameter) of the cell
`trajectory`	identifier of the DnaX track
`trajectory_length`	the time (in frames) the trajectory could be followed
`displacement_sq`	the displacement of the molecule (in pixels, as calculated by `ISBatch`)

Source

Examples

summary(DnaX_tracks)

##        x                y             frame             cell      
##  Min.   : 37.31   Min.   : 76.1   Min.   :  1.00   Min.   : 1.00  
##  1st Qu.: 85.90   1st Qu.:107.4   1st Qu.: 49.00   1st Qu.: 9.00  
##  Median :116.31   Median :125.6   Median : 91.00   Median :16.00  
##  Mean   :123.09   Mean   :125.9   Mean   : 91.25   Mean   :18.15  
##  3rd Qu.:161.98   3rd Qu.:144.5   3rd Qu.:133.00   3rd Qu.:23.00  
##  Max.   :227.67   Max.   :177.3   Max.   :181.00   Max.   :46.00  
##        l                  d             max.width       trajectory   
##  Min.   :-14.6329   Min.   :-6.3754   Min.   :10.83   Min.   : -1.0  
##  1st Qu.: -0.9614   1st Qu.:-1.9099   1st Qu.:13.17   1st Qu.:100.8  
##  Median :  1.9133   Median :-0.3906   Median :13.90   Median :284.5  
##  Mean   :  1.8945   Mean   :-0.4696   Mean   :13.82   Mean   :286.7  
##  3rd Qu.:  5.2385   3rd Qu.: 0.9774   3rd Qu.:14.53   3rd Qu.:471.0  
##  Max.   : 17.0349   Max.   : 5.5524   Max.   :15.55   Max.   :686.0  
##    max.length    trajectory_length displacement_sq    
##  Min.   :11.75   Min.   :  1.00    Min.   : 0.000000  
##  1st Qu.:24.62   1st Qu.:  3.00    1st Qu.: 0.001589  
##  Median :29.78   Median :  8.00    Median : 1.234500  
##  Mean   :29.26   Mean   : 13.01    Mean   : 2.754613  
##  3rd Qu.:33.85   3rd Qu.: 17.00    3rd Qu.: 4.000000  
##  Max.   :45.96   Max.   :102.00    Max.   :15.994000

summary(FtsZ_tracks)

##        x                y              frame             cell      
##  Min.   : 30.16   Min.   : 72.38   Min.   :  1.00   Min.   : 1.00  
##  1st Qu.: 94.05   1st Qu.:110.34   1st Qu.: 46.00   1st Qu.:10.00  
##  Median :146.93   Median :128.14   Median : 88.00   Median :16.00  
##  Mean   :139.12   Mean   :124.81   Mean   : 89.81   Mean   :18.01  
##  3rd Qu.:181.37   3rd Qu.:141.26   3rd Qu.:135.00   3rd Qu.:20.00  
##  Max.   :229.33   Max.   :176.05   Max.   :181.00   Max.   :46.00  
##        l                  d             max.width       trajectory  
##  Min.   :-18.0765   Min.   :-7.4016   Min.   :10.83   Min.   :  -1  
##  1st Qu.: -0.6594   1st Qu.:-3.0234   1st Qu.:13.30   1st Qu.: 629  
##  Median :  1.2287   Median :-0.4745   Median :13.79   Median :1524  
##  Mean   :  1.0582   Mean   :-0.2716   Mean   :13.85   Mean   :1597  
##  3rd Qu.:  2.7943   3rd Qu.: 2.3553   3rd Qu.:14.52   3rd Qu.:2490  
##  Max.   : 16.2050   Max.   : 7.1052   Max.   :15.58   Max.   :3830  
##    max.length    trajectory_length displacement_sq  
##  Min.   :10.85   Min.   : 1.0      Min.   : 0.0000  
##  1st Qu.:25.64   1st Qu.: 5.0      1st Qu.: 0.0240  
##  Median :30.28   Median :12.0      Median : 0.2020  
##  Mean   :29.74   Mean   :15.2      Mean   : 0.8358  
##  3rd Qu.:34.45   3rd Qu.:20.0      3rd Qu.: 0.7362  
##  Max.   :45.96   Max.   :93.0      Max.   :15.9850

TurnedCell4

Pixel values of FtsZ intensities per cell, retrieved by importing the FtsZ channel TIFF stack using extr_OriginalStack(), and then using the output and DnaX_mesh to connect the pixels to the meshes with extr_OriginalCells(). Only cell number 4 is included in this dataframe.

Usage

load("TurnedCell4.rda")

Format

A data frame with the following columns:

Column Name	Description
`x`	x-coordinate of the pixel
`y`	y-coordinate of the pixel
`cell`	cell identifier. unique per frame.
`frame`	frame identifier. in this case, an image was taken every 20 seconds, so 1 frame corresponds to 20s.
`max.width`	maximum cell width in pixels
`max.length`	the maximum cell length of the given cell
`pointN`	number of specific pixel. unique per cell and frame
`values`	intensity of the pixel
`X_rot`	pixel x coordinate when the cell is turned so that the length axis is horizontal and mid-cell is at 0,0.
`Y_rot`	pixel y coordinate when the cell is turned so that the length axis is horizontal and mid-cell is at 0,0.
`xt`	the point marking one corner of the square pixel (x-coordinate)
`yt`	the point marking one corner of the square pixel (y-coordinate)
`area`	the cell area (pixel squared)

Source

Example

bactMAP::bactKymo(TurnedCell4, timeD=TRUE, sizeAV=TRUE, mag="100x_DVMolgen")

## [[1]]

The Van-FL dataset

Description

As the DnaX/FtsZ-set, the Van-FL set is a subset of a dataset generated and analyzed for van Raaphorst, Kjos & Veening, 2017. I included this dataset in BactMAP as an example of a dataset with objects and two different conditions, so it is a good set to try out functions as plotObjects() or plotOverlay(). The dataset contains 2 different cells: Wild Type (“WT”) S. pneumoniae and S. pneumoniae lacking the gene mapZ (“DM”). These cells where treated with fluorescent vancomycin and imaged. The septa were detected as objects, the cells as meshes using Oufti.

The WT-subset

an object_relative dataframe containing the coordinates and shape descriptors of the fluorescent objects (septa as stained by fluorescent vancomycin) in Wild Type pneumococcus, and a mesh dataframe containing the coordinates and shape descriptors of the pneumococcal cells.

Usage

#objects
VanFL_objWT

#mesh
VanFL_meshWT

Source

Examples

For more examples, see plotObjects()

summary(VanFL_objWT)

##      frame            cell         max.length        obnum      
##  Min.   :1.000   Min.   :  1.0   Min.   :17.92   Min.   :1.000  
##  1st Qu.:2.000   1st Qu.: 60.0   1st Qu.:24.74   1st Qu.:1.000  
##  Median :5.000   Median :155.0   Median :26.77   Median :1.000  
##  Mean   :4.867   Mean   :119.5   Mean   :28.18   Mean   :1.506  
##  3rd Qu.:8.000   3rd Qu.:173.0   3rd Qu.:29.50   3rd Qu.:2.000  
##  Max.   :9.000   Max.   :189.0   Max.   :44.45   Max.   :4.000  
##                                  NA's   :26      NA's   :5      
##       num            obpath          obID             max.width    
##  Min.   :  1.0   Min.   : 1.00   Length:3765        Min.   :14.39  
##  1st Qu.: 63.0   1st Qu.: 7.00   Class :character   1st Qu.:16.45  
##  Median :148.0   Median :14.00   Mode  :character   Median :17.03  
##  Mean   :154.4   Mean   :16.86                      Mean   :16.92  
##  3rd Qu.:244.0   3rd Qu.:22.00                      3rd Qu.:17.44  
##  Max.   :328.0   Max.   :84.00                      Max.   :18.61  
##                  NA's   :5                          NA's   :26     
##       Dum                Lmid              ob_out_x       
##  Min.   :-5.93760   Min.   :-1.047667   Min.   :-1.55394  
##  1st Qu.:-0.03004   1st Qu.:-0.095982   1st Qu.:-0.21668  
##  Median : 0.01509   Median : 0.008118   Median :-0.01836  
##  Mean   :-0.04567   Mean   :-0.028105   Mean   :-0.03678  
##  3rd Qu.: 0.07370   3rd Qu.: 0.072275   3rd Qu.: 0.18314  
##  Max.   : 2.03162   Max.   : 0.759431   Max.   : 1.41061  
##  NA's   :31         NA's   :31          NA's   :31        
##     ob_out_y            pole1             pole2            max_um     
##  Min.   :-0.87521   Min.   :-1.4348   Min.   :0.5784   Min.   :1.157  
##  1st Qu.:-0.20162   1st Qu.:-0.9520   1st Qu.:0.7986   1st Qu.:1.597  
##  Median : 0.04066   Median :-0.8639   Median :0.8639   Median :1.728  
##  Mean   : 0.03150   Mean   :-0.9095   Mean   :0.9095   Mean   :1.819  
##  3rd Qu.: 0.27449   3rd Qu.:-0.7986   3rd Qu.:0.9520   3rd Qu.:1.904  
##  Max.   : 0.75336   Max.   :-0.5784   Max.   :1.4348   Max.   :2.870  
##  NA's   :31         NA's   :26        NA's   :26       NA's   :26     
##      maxwum      
##  Min.   :0.9289  
##  1st Qu.:1.0621  
##  Median :1.0993  
##  Mean   :1.0924  
##  3rd Qu.:1.1256  
##  Max.   :1.2012  
##  NA's   :26

bactMAP::plotRaw(meshdata=VanFL_meshWT)

The DM-subset

an object_relative dataframe containing the coordinates and shape descriptors of the fluorescent objects (septa as stained by fluorescent vancomycin) in pneumococcus where mapZ is replaced for a chloramphenical resistance marker, and a mesh dataframe containing the coordinates and shape descriptors of the same **pneumococcal cells. **

Usage

#objects
VanFL_objDM

#mesh
VanFL_meshDM

Source

Examples

For more examples, see plotOverlay()

summary(VanFL_objDM)

##      frame             cell         max.length        obnum      
##  Min.   : 1.000   Min.   : 3.00   Min.   :18.50   Min.   :1.000  
##  1st Qu.: 4.000   1st Qu.:25.00   1st Qu.:23.68   1st Qu.:1.000  
##  Median : 7.000   Median :40.00   Median :27.49   Median :1.000  
##  Mean   : 6.588   Mean   :37.15   Mean   :29.50   Mean   :1.763  
##  3rd Qu.:10.000   3rd Qu.:52.00   3rd Qu.:35.72   3rd Qu.:2.000  
##  Max.   :10.000   Max.   :60.00   Max.   :43.61   Max.   :5.000  
##                                   NA's   :51      NA's   :3      
##       num            obpath          obID             max.width    
##  Min.   :  3.0   Min.   : 1.00   Length:1908        Min.   :15.13  
##  1st Qu.: 64.0   1st Qu.: 8.00   Class :character   1st Qu.:17.14  
##  Median :137.0   Median :15.00   Mode  :character   Median :18.00  
##  Mean   :141.8   Mean   :17.33                      Mean   :18.09  
##  3rd Qu.:220.0   3rd Qu.:24.00                      3rd Qu.:19.29  
##  Max.   :262.0   Max.   :73.00                      Max.   :20.36  
##                  NA's   :3                          NA's   :51     
##       Dum                Lmid             ob_out_x       
##  Min.   :-4.61623   Min.   :-0.93076   Min.   :-1.09986  
##  1st Qu.:-0.05215   1st Qu.:-0.24524   1st Qu.:-0.22804  
##  Median : 0.02144   Median : 0.00473   Median :-0.03272  
##  Mean   : 0.14133   Mean   :-0.01610   Mean   :-0.01446  
##  3rd Qu.: 0.29018   3rd Qu.: 0.13257   3rd Qu.: 0.20792  
##  Max.   : 5.52891   Max.   : 1.09036   Max.   : 1.45269  
##  NA's   :54         NA's   :54         NA's   :54        
##     ob_out_y            pole1             pole2            max_um     
##  Min.   :-0.80697   Min.   :-1.4076   Min.   :0.5972   Min.   :1.194  
##  1st Qu.:-0.20679   1st Qu.:-1.1530   1st Qu.:0.7644   1st Qu.:1.529  
##  Median : 0.07488   Median :-0.8873   Median :0.8873   Median :1.775  
##  Mean   : 0.06105   Mean   :-0.9521   Mean   :0.9521   Mean   :1.904  
##  3rd Qu.: 0.31968   3rd Qu.:-0.7644   3rd Qu.:1.1530   3rd Qu.:2.306  
##  Max.   : 1.04965   Max.   :-0.5972   Max.   :1.4076   Max.   :2.815  
##  NA's   :54         NA's   :51        NA's   :51       NA's   :51     
##      maxwum      
##  Min.   :0.9769  
##  1st Qu.:1.1066  
##  Median :1.1622  
##  Mean   :1.1679  
##  3rd Qu.:1.2451  
##  Max.   :1.3144  
##  NA's   :51

bactMAP::plotRaw(meshdata=VanFL_meshDM)

example datasets in bactmap - veeninglab/BactMAP GitHub Wiki

The ssbB-set

Description

ssbB_meanfluo

Usage

Format

Source

Example

ssbB_phylos

Usage

Format

Source

Example

ssbB_network

Usage

Format

Source

Examples

The DnaX/FtsZ-set

Description

DnaX_mesh

Usage

Format

Source

Example

DnaX_tracks & FtsZ_tracks

Usage

Format

Source

Examples

TurnedCell4

Usage

Format

Source

Example

The Van-FL dataset

Description

The WT-subset

Usage

Source

Examples

The DM-subset

Usage

Source

Examples

⚠️ **GitHub.com Fallback** ⚠️

⚠️ GitHub.com Fallback ⚠️