subsetting matrix elements and creating a histogram
I have some data from CITEseq experiment (Umi.adt) I want to look at. The matrix is 24 x 200000 where the rows are antibody names and the columns are barcodes (cells). Many of the cells have few, little to no UMI counts.
I want to make a histogram with frequency on the y axis, and UMI count on the x-axis.
I can sum the UMI's for each cell by going x <- colSums(Umi.adt) but how do I take this data and plot the frequency of each total UMI count across this data set?
plotting hist(x) gives one large column of frequency 250000
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It seems im having some trouble understanding this data structure:
When I make
x <- colSums(Umi.adt)x is a vector of type double, but it seems to have 2 dimensions, one is the tags, and the other is the sums that we calculated previously. When I doattributes (x)I get..... $names [1] "CGATGGCTCGCACTCT" "CTCATGCGTCACCACG" "NTAGGTTCACAGTCGC" "CCTCAACAGCGGGTAT" "TGCATTGTAGGATATA" etc.........................when I run
head(x)I get....CGATGGCTCGCACTCT CTCATGCGTCACCACG NTAGGTTCACAGTCGC CCTCAACAGCGGGTAT TGCATTGTAGGATATA TGTTACTGTATCGAAA 1 14 1 7 2 96
When I run hist(x) I think the program is using the tags? Im not really sure whats happening
Here if we just look at the first data point in the vector it has
x[1] CGATGGCTCGCACTCT 1
How would you separate out the number from the string?
The data point in this case is characterized by a name and by a value. You don't need to separate value from name. You can create a name-less vector for example with
y=as.numeric(x)but it's not required. What doessummary(x)show?Thanks; I only have access to the data set I ran on 6000 cells now, so the matrix is 24 x 6000 but its the same thing essentially. The histogram shows one giant bar at frequency 6000 and then some smaller ones. Summary(x) shows:
and is the same whether I run as is or use
y=as.numeric(x)as you suggestedhere is the histogram
Data point 5625 is dominating the histogram cell size. You can zoom in for example with
hist(x,breaks=1000,xlim=c(0,400))or just exclude outlier/s. The issue here is R and plot related. You should explore the reason for the outlier though.Ahhh yes I have it now!
Thank you so much