I have generated some gene signatures of cell states from an single-cell experiment (signatures A-H)
I want to select 1 value per cell from the gene signatures to represent the cell state. However, the signature scores from different states have different distributions so I don’t think it would be appropriate to just choose the max score for each cell.
I have made the scores avaialble:
<code>test.df <- read.csv("https://docs.google.com/spreadsheets/d/e/2PACX-1vS5jLScYx4AaCiqRZwDqnqf41ozSzvLMLOWUU5VLT2FJ7XOBWbjJe_NLMOkK7-ndZ7m1LNFcD8ARB5L/pub?output=csv")
library(ggplot2)
library(pals)
kelly.cols <- kelly(22)[-c(1:2)]
ggplot(test.df,
mapping = aes(x = value, fill = variable)) +
geom_histogram(binwidth = 0.01) +
theme_bw() +
theme(panel.grid.minor.y = element_blank(),
panel.grid.major.y = element_blank(),
panel.grid.minor.x = element_line(linetype = "dotted"),
panel.grid.major.x = element_line(linetype = "dotted")) +
scale_fill_manual(values = kelly.cols[1:8])
</code>
<code>test.df <- read.csv("https://docs.google.com/spreadsheets/d/e/2PACX-1vS5jLScYx4AaCiqRZwDqnqf41ozSzvLMLOWUU5VLT2FJ7XOBWbjJe_NLMOkK7-ndZ7m1LNFcD8ARB5L/pub?output=csv")
library(ggplot2)
library(pals)
kelly.cols <- kelly(22)[-c(1:2)]
ggplot(test.df,
mapping = aes(x = value, fill = variable)) +
geom_histogram(binwidth = 0.01) +
theme_bw() +
theme(panel.grid.minor.y = element_blank(),
panel.grid.major.y = element_blank(),
panel.grid.minor.x = element_line(linetype = "dotted"),
panel.grid.major.x = element_line(linetype = "dotted")) +
scale_fill_manual(values = kelly.cols[1:8])
</code>
test.df <- read.csv("https://docs.google.com/spreadsheets/d/e/2PACX-1vS5jLScYx4AaCiqRZwDqnqf41ozSzvLMLOWUU5VLT2FJ7XOBWbjJe_NLMOkK7-ndZ7m1LNFcD8ARB5L/pub?output=csv")
library(ggplot2)
library(pals)
kelly.cols <- kelly(22)[-c(1:2)]
ggplot(test.df,
mapping = aes(x = value, fill = variable)) +
geom_histogram(binwidth = 0.01) +
theme_bw() +
theme(panel.grid.minor.y = element_blank(),
panel.grid.major.y = element_blank(),
panel.grid.minor.x = element_line(linetype = "dotted"),
panel.grid.major.x = element_line(linetype = "dotted")) +
scale_fill_manual(values = kelly.cols[1:8])
I would like some advice on how to call the state based on the signature scores provided.