flowCore | Core flow cytometry infrastructure | Theme library
kandi X-RAY | flowCore Summary
kandi X-RAY | flowCore Summary
Install the devtools package and then do devtools::install_github("RGLab/flowCore"). You may need to install other dependencies as well.
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Community Discussions
Trending Discussions on flowCore
QUESTION
I'm new to flowCore + R. I would like to mimic a histogram plot after gating that can be manually done in FlowJo software. I got something similar but it doesn't look quite right because it is a "density" plot and is shifted. How can I get the x axis to shift over and look similar to how FlowJo outputs the plot? I tried reading this document but couldn't find a plot similar to the one in FlowJo: howtoflowcore Appreciate any guidance. Thanks.
code snippet: ...ANSWER
Answered 2021-May-18 at 09:27The reason that for the "shift" is that the x axis is logarithmic (base 10) in the flowJo graph. To achieve the same result in R, add
QUESTION
I am trying to set the x limits on a ggcyto(ggplot2) plot, but it doesn't seem to work. The x-limit that I set is squished all the way to the right and there is a lot of empty space. Not sure what else to try. I tried setting biexp scale but it looked the same.
...ANSWER
Answered 2021-Mar-24 at 15:45Don't have your data so can't reproduce the weird axis. I would check your data for negative values. Also the ggcyto
wrapper has some restrictions on your limits.
Using an example data below, I set 2 values on the first column "FSC" to be -999, and I get a similar error:
QUESTION
I work with the package flowCore
found in Bioconductor, which reads my data files in an S4 class format. You can type library(flowCore)
and then data(GvHD)
which loads an example dataset. When you type GvHD
you can see that this dataset is made out of 35 experiments, which can be accessed individually by typing for example GvHD[[1]]
.
Now I am trying to delete two columns FSC-H
and SSC-H
from all the experiments, but I have been unsuccessful.
I have tried myDataSet<- within(GvHD, rm("FSC-H","SSC-H"))
but it doesn't work. I would greatly appreciate any help.
ANSWER
Answered 2020-Apr-15 at 07:15rm
isn't meant for removing columns. The normal procedure is to assign NULL
to that column:
QUESTION
I have a directory containing 28 FCS files (raw data from a flow cytometer). I am converting the list of 'flowFrame' objects into a list of data frames, and I would like to create a column in each data frame that refers to the file name.
...ANSWER
Answered 2020-Feb-13 at 16:21If we need to get all the description, elements loop over the list
with lapply/sapply/Map
and use anonymous function call
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