Code color in graphs about lncrna_bc HOT 12 CLOSED

Hi Laura,
I can't access the data of the graphic

1. you need to save it into .csv
2. you need to put it into the data folder
3. In your R code you need to import these data

from lncrna_bc.

Hi laura

To import .csv files you have to do this

name_df <- read.csv("name_your_file.csv")

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Hi Cris,

The command to export a table is:
write.csv(table_in_R$columns, "name.csv")

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Hi! I've already uploaded the .csv file

and also I corrected the script. Thank you!!

from lncrna_bc.

May be you can check this if you have header and others considers:
ERROR: Nine number changed by )
read.table(file, header = FALSE, sep = "", quote = ""'"9
TRUE:
read.table(file, header = FALSE, sep = "", quote = ""'")

from lncrna_bc.

Hi! I've indicated the header but I don't know how to indicate rownames... help!

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https://github.com/opetchey/RREEBES/wiki/Reading-data-and-code-from-an-online-github-repository

How to upload a file in R from Github

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Hi! I added a line in the script,
VPSol <- data.frame(BCresultsNR$log2FoldChange, BCresultsNR$sig, row.names = rownames(BCresultsNR)) ##Creates a data frame with coordinates##
This generates a data frame with coordinates data. For colors, I would like to categorize data following this:

Color 1: $log2FC > 1.5, $sig <0.05
Color 2: $log2FC < -1.5, $sig <0.05
Color 3: $log2FC > 1.5, $sig > 0.05
Color 4: $log2FC < -1.5, $sig >0.05
Color 5: 0 < $log2FC< 1.5, $sig > 0.05
Color 6: -1.5 < $log2FC < 0
Thanks!!!

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Hi Laura

I have the answer, you have to do this:

##Rename the columns to simplify the dataframe##

VPSol <- VPSol %>% rename(FoldChange = BCresultsNR.log2FoldChange, p_value = BCresultsNR.sig)

##Create a column with colors depending on the value of Fold Change and p-value##  

VPSol$color <- ifelse((VPSol$FoldChange > 1.5) & (VPSol$p_value < 0.05), "Col_1",
                      ifelse((VPSol$FoldChange < -1.5) & (VPSol$p_value < 0.05), "Col_2",
                             ifelse((VPSol$FoldChange > 1.5) & (VPSol$p_value > 0.05), "Col_3",
                                    ifelse((VPSol$FoldChange < -1.5) & (VPSol$p_value > 0.05), "Col_4",
                                           ifelse((VPSol$FoldChange < 1.5) & (VPSol$p_value > 0.05), "Col_5", "Col_6")))))

##Create plot##
ggplot(VPSol, aes(x=FoldChange, y=p_value)) +
  geom_point(aes(colour = color)) 

I can run it on my computer, I hope you can also run it. In ggplot we can put the lines to divide the grid, but I don't know how to you want it.

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Hi Laura

I finally found a way to upload the dataframe in R from GitHub!

# upload the csv file
# the first column need to have a name - I modified the csv file by adding "sample" on the first column 
# the link need to be the raw data by clicking "view raw"

library (readr)
urlfile="https://raw.githubusercontent.com/LauraMCE/lncRNA_BC/master/Transcriptome/Data_1_Diff_genes.csv"
BCData<-read_csv(url(urlfile))

# transform the table into a dataframe, indicating that the first column is the row names
BCData <- as.data.frame(BCData)
rownames(BCData) <- BCData[, 1]
BCData <- BCData[, -1]

#verify that the data are correct
head(BCData)
row.names(BCData)
colnames(BCData)

It works on my computer. Try on your own and if it works, modify the code in Github so that everyone can access the data and make the graphic.

Good job everyone, we are getting close!

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Hi Laura,
Don't forget to reply and if no further issues occur, close the issue!

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Hi, @camillethuyentruong ! The code you provided me worked perfectly, and it is already uploaded in the code. Thanks!
Hi, @cristoichkov ! Thanks for the script. I did some changes that you can see here, but... It worked!! I have now a very nice Volcano Plot with a lot of colors. Thanks everybody @VeroIarrachtai @camillethuyentruong for helping me!!

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