Question: FlowViz working though is showing as attached
0
gravatar for rocmanik
4.9 years ago by
rocmanik0
United States
rocmanik0 wrote:

Greetings! M.S. in Biology student looking to wrap my head around Flow cytometry data analysis via R.

I have done some messing around and previously got a simple plot of my data and some channels. I set out to isolate some replicates and look at those. Everything seems fine except for my error message during an attempt to plot something that should in fact plot...

Basically I have no idea why R tells me flowViz is not attached when session is showing that it is?





R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] grid      splines   parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] flowDensity_1.0.0       BiocInstaller_1.16.1    GGally_0.4.8            ggplot2_1.0.0         
[5] flowStats_3.24.0        flowWorkspace_3.12.04   gridExtra_0.9.1         ncdfFlow_2.12.0       
[9] BH_1.54.0-5             RcppArmadillo_0.4.500.0 cluster_1.15.3          mvoutlier_2.0.5       
[13] sgeostat_1.0-25         fda_2.4.3               Matrix_1.1-4            flowViz_1.30.0        
[17] lattice_0.20-29         Biobase_2.26.0          BiocGenerics_0.12.1     flowCore_1.32.1        

loaded via a namespace (and not attached):
[1] bitops_1.0-6          car_2.0-22            caTools_1.17.1        chron_2.3-45        
[5] colorspace_1.2-4      corpcor_1.6.7         data.table_1.9.4      DEoptimR_1.0-2      
[9] digest_0.6.4          gdata_2.13.3          GEOmap_2.2-2          gplots_2.14.2       
[13] graph_1.44.0          gtable_0.1.2          gtools_3.4.1          hexbin_1.27.0       
[17] IDPmisc_1.1.17        KernSmooth_2.23-13    ks_1.9.3              latticeExtra_0.6-26 
[21] MASS_7.3-35           MBA_0.0-8             misc3d_0.8-4          munsell_0.4.2       
[25] mvtnorm_1.0-1         nnet_7.3-8            pcaPP_1.9-60          pls_2.4-3           
[29] plyr_1.8.1            proto_0.3-10          RColorBrewer_1.0-5    Rcpp_0.11.3         
[33] reshape_0.8.5         reshape2_1.4          RFOC_3.3-3            rgl_0.95.1158       
[37] Rgraphviz_2.10.0      robCompositions_1.9.0 robustbase_0.92-2     RPMG_2.1-5          
[41] rrcov_1.3-4           RSEIS_3.3-3           Rwave_2.2             scales_0.2.4        
[45] sp_1.0-16             splancs_2.01-36       stats4_3.1.1          stringr_0.6.2       
[49] tools_3.1.1           XML_3.98-1.1          zlibbioc_1.12.0     

#the flowSet and error message
Cneg
A flowSet with 3 experiments.

  column names:
  SS EV FL1 FL2 FL3 TIME
> plot(Cneg)
For plotting, please attach the 'flowViz' package.
   i.e., 'library(flowViz)'

flowviz • 894 views
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by rocmanik0
Answer: FlowViz working though is showing as attached
2
gravatar for Greg Finak
4.9 years ago by
Greg Finak150
(Private Address)
Greg Finak150 wrote:
Did you explicitly `library(flowViz)`? Also, `plot` is not how you plot a flowSet in `flowViz`. You'll want `xyplot`, and you'll want to specify the channels. Have a look at the package vignette here http://www.bioconductor.org/packages/release/bioc/vignettes/flowViz/inst/doc/filters.html It provides plenty of examples. I'd also recommend d looking into the GatingSet infrastructure in flowWorkspace as it greatly simplifies managing and plotting you flow data, and it makes use of all the existing infrastructure in flowViz and flowCore. Greg
ADD COMMENTlink written 4.9 years ago by Greg Finak150
Answer: FlowViz working though is showing as attached
0
gravatar for rocmanik
4.9 years ago by
rocmanik0
United States
rocmanik0 wrote:

Definitely looking into this. I did explicitly 'library(flowViz)' and plot for some reason worked in another situation. But even then..it should tell me that flowViz is loaded or plot isn't how it's used. Will report back with an edit. Also happy holidays and thank you for your input. Duy

edit: following the instructions i run into something else interesting, when I go to set my flowset as data(Cneg) when I was trying to reproduce these lines from the examples you linked:

data(GvHD)
head(pData(GvHD))

The error message
In data(Cneg) : data set ‘Cneg’ not found

xyplot worked when I told it to compare some channels(which is what I needed) So I will continue from there. It just feels like something is inherently wrong with the output of my data from my flow?

subset of replicates:

> Cneg
A flowSet with 3 experiments.

  column names:
  SS EV FL1 FL2 FL3 TIME
> Cneg[[1]] #summary of each frame with quartiles
flowFrame object 'S3Cneg10minR1_10252014.LMD'
with 13957 cells and 6 observables:
    name              desc range minRange maxRange
$P1   SS      Side Scatter  1024 1.009044    10000
$P2   EV Electronic Volume  1024 0.000000     1023
$P3  FL1  FL1 Fluorescence  1024 1.009044    10000
$P4  FL2  FL2 Fluorescence  1024 1.009044    10000
$P5  FL3  FL3 Fluorescence  1024 1.009044    10000
$P6 TIME              Time  1024 0.000000     1023
316 keywords are stored in the 'description' slot
> Cneg[[2]] #summary of each frame with quartiles
flowFrame object 'S3Cneg10minR2_10252014.LMD'
with 19839 cells and 6 observables:
    name              desc range minRange maxRange
$P1   SS      Side Scatter  1024 1.009044    10000
$P2   EV Electronic Volume  1024 0.000000     1023
$P3  FL1  FL1 Fluorescence  1024 1.009044    10000
$P4  FL2  FL2 Fluorescence  1024 1.009044    10000
$P5  FL3  FL3 Fluorescence  1024 1.009044    10000
$P6 TIME              Time  1024 0.000000     1023
316 keywords are stored in the 'description' slot
> Cneg[[3]] #summary of each frame with quartiles
flowFrame object 'S3Cneg10minR3_10252014.LMD'
with 39266 cells and 6 observables:
    name              desc range minRange maxRange
$P1   SS      Side Scatter  1024 1.009044    10000
$P2   EV Electronic Volume  1024 0.000000     1023
$P3  FL1  FL1 Fluorescence  1024 1.009044    10000
$P4  FL2  FL2 Fluorescence  1024 1.009044    10000
$P5  FL3  FL3 Fluorescence  1024 1.009044    10000
$P6 TIME              Time  1024 0.000000     1023
316 keywords are stored in the 'description' slot
ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by rocmanik0
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