When I run the MAGeCKFlute, the output graph and data are not based on my own data but the model data. For Example:

> library('MAGeCKFlute')
Loading required package: ggplot2
Loading required package: gridExtra

Registered S3 method overwritten by 'enrichplot':
  method               from
  fortify.enrichResult DOSE
##############################################################################
Pathview is an open source software package distributed under GNU General
Public License version 3 (GPLv3). Details of GPLv3 is available at
http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
formally cite the original Pathview paper (not just mention it) in publications
or products. For details, do citation("pathview") within R.

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
license agreement (details at http://www.kegg.jp/kegg/legal.html).
##############################################################################
MAGeCKFlute is an open source software package. Particullary, users are
required to formally cite the original MAGeCKFlute paper in publications or
products. For details, do citation("MAGeCKFlute") within R.
> countsummary=read.table('~/DataProcessing/magecksnakes/mageckcount/result.countsummary.txt') 
> View(countsummary)
1   File    Label   Reads   Mapped  Percentage  TotalsgRNAs Zerocounts  GiniIndex   NegSelQC    NegSelQCPval    NegSelQCPvalPermutation NegSelQCPvalPermutationFDR  NegSelQCGene
2   G20.bam G20 5214605 3602121 0.6908  11107   56  0.07057 0   1   1   1   0.0
3   G1.bam  G1  4272051 3232724 0.7567  11107   5   0.05494 0   1   1   1   0.0
Showing 1 to 3 of 3 entries, 13 total columns
##Data above are my Data created from mageck
##then I started to run MAGeckFlute
> data("countsummary")
> head(countsummary)
                                  File    Label    Reads   Mapped Percentage
1 ../data/GSC_0131_Day23_Rep1.fastq.gz day23_r1 62818064 39992777     0.6366
2  ../data/GSC_0131_Day0_Rep2.fastq.gz  day0_r2 47289074 31709075     0.6705
3  ../data/GSC_0131_Day0_Rep1.fastq.gz  day0_r1 51190401 34729858     0.6784
4 ../data/GSC_0131_Day23_Rep2.fastq.gz day23_r2 58686580 37836392     0.6447
  TotalsgRNAs Zerocounts GiniIndex NegSelQC NegSelQCPval NegSelQCPvalPermutation
1       64076         57   0.08510        0            1                       1
2       64076         17   0.07496        0            1                       1
3       64076         14   0.07335        0            1                       1
4       64076         51   0.08587        0            1                       1
  NegSelQCPvalPermutationFDR NegSelQCGene
1                          1            0
2                          1            0
3                          1            0
4                          1            0

the table is not my table any more and the same problem occurred when I run FluteRRA, the output graphs are not based on my data.

When you run the command data("countsummary") it loads the example data from the MAGeCKFlute package, and this overwrites your existing countsummary table.

It's common to see this used in package vignettes as it allows the code to be run on some example dataset, but you don't have to run that step if you have your own data to provide instead.