rankNet: Wrong text color on axis.text when using parameter signaling or pairLR

[Bejsernia]

• The same error reported in #133

When using parameter signaling or pairLR in rankNet, the color of text on the axis is different from the original one.

eg. runing command 1:

rankNet(object, mode = "comparison", measure = "weight",comparison = c(1,2), stacked = T, do.stat = TRUE)

result:

runing command 2:

rankNet(object, mode = "comparison", measure = "weight", signaling = c("NOTCH","VWF"),comparison = c(1,2), stacked = T, do.stat = TRUE)

result:

Solution:

• Fix the rankNet function, put the colors.text part after the subset part: @sqjin

colors.text part:

https://github.com/jinworks/CellChat/blob/346fb615aaefa3c1a2830ec2fe3a933c5f723c83/R/analysis.R#L1301-L1310

subset part:

https://github.com/jinworks/CellChat/blob/346fb615aaefa3c1a2830ec2fe3a933c5f723c83/R/analysis.R#L1319-L1328

Final codes:

modify_rankNet <- function(object, ......) {
    ......

    for (i in 1:length(pair.name.all)) {
      df.t <- df[df$name == pair.name.all[i], "contribution"]
      if (sum(df.t) == 0) {
        df <- df[-which(df$name == pair.name.all[i]), ]
      }
    }
    
    if ((slot.name == "netP") && (!is.null(signaling))) {
      df <- subset(df, name %in% signaling)
    } else if ((slot.name == "netP") &&(!is.null(pairLR))) {
      stop("You need to set `slot.name == 'net'` if showing specific L-R pairs ")
    }
    if ((slot.name == "net") && (!is.null(pairLR))) {
      df <- subset(df, name %in% pairLR)
    } else if ((slot.name == "net") && (!is.null(signaling))) {
      stop("You need to set `slot.name == 'netP'` if showing specific signaling pathways ")
    }
    
    if (length(comparison) == 2) {
      if (do.stat) {
        colors.text <- ifelse((df$contribution.relative < 1-tol) & (df$pvalues < cutoff.pvalue), color.use[2], ifelse((df$contribution.relative > 1+tol) & df$pvalues < cutoff.pvalue, color.use[1], "black"))
      } else {
        colors.text <- ifelse(df$contribution.relative < 1-tol, color.use[2], ifelse(df$contribution.relative > 1+tol, color.use[1], "black"))
      }
    } else {
      message("The text on the y-axis will not be colored for the number of compared datasets larger than 3!")
      colors.text = NULL
    }
    
    if (stacked) {
      gg <- ggplot(df, aes(x=name, y=contribution, fill = group)) + geom_bar(stat="identity",width = bar.w, position ="fill") # +
      # xlab("") + ylab("Relative information flow") #+ theme(axis.text.x = element_blank(),axis.ticks.x = element_blank())
      #  scale_y_discrete(breaks=c("0","0.5","1")) +
      if (measure == "weight") {
        gg <- gg + xlab("") + ylab("Relative information flow")
      } else if (measure == "count") {
        gg <- gg + xlab("") + ylab("Relative number of interactions")
      }
      ......
}

For users' temporary solution, copy the code of the rankNet function and fix it by assigning a modify_rankNet function

runing command 3:

modify_rankNet(object, mode = "comparison", measure = "weight", signaling = c("NOTCH","VWF"),comparison = c(1,2), stacked = T, do.stat = TRUE)

result: